Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Wolbachia infection causes male-specific death in Ostrinia furnacalis , but its removal from infected strains results in female-specific death instead of restoring 1:1 sex ratio, suggesting that cytoplasmic Wolbachia , not the host genome, primarily determines femaleness in infected strains. This phenomenon is a striking example of the evolutionary outcome of cytoplasmic sex determination, potentially arising from prolonged host-symbiont co-evolution. Although we recently identified Oscar, the Wolbachia -encoded male-killing effector targeting the host masculinizing factor OfMasc in Ostrinia moths, inactivation or loss of the host’s endogenous feminizer remains unknown. Here we identify a W-linked primary feminizer, OfFem piRNA, which targets an mRNA encoding an OfMasc-interacting protein Ofznf-2. We demonstrate that Ofznf-2 is essential for both masculinization and dosage compensation. We also show that OfFem piRNA is entirely absent in the Wolbachia -infected lineage, providing molecular evidence that a male-killing Wolbachia hijacks the host feminizing piRNA function by acquiring the Oscar protein during prolonged endosymbiosis.

DOI： 10.1038/s41467-025-67993-x

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Other Link： https://www.nature.com/articles/s41467-025-67993-x

DOI： 10.1101/2025.11.01.685978

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Publishing type：Research paper (scientific journal)  

DOI： 10.1128/mra.00722-25

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Language：English   Publishing type：Research paper (scientific journal)  

INTRODUCTION: DMRT1 on the Z chromosome is a conserved male sex-determining gene in birds. In chickens, a representative model species of Neognathae, the function of DMRT1 has been well characterized. In contrast, Palaeognathae species such as the emu possess less differentiated sex chromosomes and thus provide a valuable system for investigating avian sex determination, yet molecular studies remain limited. We investigated the timing of sex determination and the expression of key genes involved in gonadal differentiation in emu, and further characterized DMRT1 variants. METHODS: Sex determination stage was identified by anatomical comparison of male and female embryonic gonads. Expression of seven genes (DMRT1, AMH, SOX9, NR5A1, FOXL2, CYP19A1, and RSPO1) was examined by mRNA-seq and RT-PCR. DMRT1 splicing variants were predicted by in silico analysis and 3' RACE was used to identify alternative polyadenylation (APA) variants. RESULTS: The gonadal differentiation occurred at HH25-28 based on gonadal morphology. Gene expression analysis revealed emu-specific patterns not observed in chickens. Notably, RSPO1 was highly expressed in females at HH24-25, preceding DMRT1 expression in males at HH28-29, suggesting ovarian differentiation begins earlier. We identified three splicing variants and four APA variants of DMRT1, with variant 1 predominant during gonadal development. CONCLUSION: These findings suggest that while molecular sex differentiation mechanisms are largely conserved between Palaeognathae and Neognathae, they differ in parts. In particular, early RSPO1 expression may initiate ovarian differentiation prior to testis determination by DMRT1. The presence of emu-specific DMRT1 variants further indicates possible species-specific mechanisms in testis development.

DOI： 10.1159/000548251

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Publishing type：Research paper (scientific journal)  

DOI： 10.1111/nph.70380

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DOI： 10.1098/rspb.2025.1306

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Language：English   Publishing type：Research paper (scientific journal)  

Chromosomal sex-determining systems with male heterogamety include actively male-determining-Y and X-A balance systems, both of which are found in animals and plants. The sex-determining genes have been identified in several active-Y plant systems, but the evolution and functioning of X-A balance systems remains mysterious. Here we sequenced and compared the genomes of two hop species. The evolution of the hop X-A balance system involved an ancient recombination suppression event across a large X chromosome region shared by both species. In one species, an autosome fused to this ancestral sex chromosome, and recombination was subsequently suppressed again. The two evolutionary strata created in this neo-X have degenerated to different degrees and evolved correspondingly different dosage compensation levels that correlate with histone modification patterns. Finally, we identified an X-specific ETR1-like ethylene receptor in the ancestral X region. Its dosage may affect sex determination, as part of the counting mechanism of this X-A balance system.

DOI： 10.1038/s41477-025-02017-6

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1093/dnares/dsaf012

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1093/molbev/msaf102

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Language：English   Publishing type：Research paper (scientific journal)  

Some plants have massive sex-linked regions. To test hypotheses about their evolution, we sequenced the genome of Silene latifolia, in which giant heteromorphic sex chromosomes were first discovered in 1923. It has long been known that the Y chromosome consists mainly of a male-specific region that does not recombine with the X chromosome and carries the sex-determining genes and genes with other male functions. However, only with a whole Y chromosome assembly can candidate genes be validated experimentally and their locations determined and related to the suppression of recombination. We describe the genomic changes as the ancestral chromosome evolved into the current XY pair, testing ideas about the evolution of large nonrecombining regions and the mechanisms that created the present recombination pattern.

DOI： 10.1126/science.adk9074

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society for Plant Cell and Molecular Biology  

DOI： 10.5511/plantbiotechnology.24.0510a

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Publishing type：Research paper (scientific journal)   Publisher：Cold Spring Harbor Laboratory  

Abstract

In eukaryotes, mRNAs with long poly(A) tails are translationally active, whereas deadenylation of the tails decreases translation and uridylation of the short poly(A) tails causes the mRNA to be degraded. In this study, we confirmed that maternal cyclin B mRNAs with long poly(A) tails in blastula embryos of invertebrate starfish were deadenylated and uridylated, followed by decay. In starfish oocytes, however, cyclin B mRNAs with uridylated short poly(A) tails are stable. They are polyadenylated and translationally active immediately following hormonal stimulation for resumption of meiosis. Similarly, maternal ribosomal protein mRNAs, Rps29 and Rpl27a, which become uridylated following deadenylation upon hormonal stimulation, remain stable even after fertilisation and early development. At the morula stage, the uridylated maternal ribosomal protein mRNAs are modified to yield non-canonical poly (A) tails rich in U and G residues in the 5’ region and in A residues at the 3’ end, rendering them translationally active. These results indicate that the fates of uridylated mRNAs in starfish are decay and/or recycling.

DOI： 10.3390/biom14121610

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DOI： 10.1101/2024.11.03.621702

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Language：English   Publishing type：Research paper (scientific journal)  

<jats:title>Abstract</jats:title><jats:p>Males and females share most of the genome, but many animals show different phenotypes between the sexes, known as sexual dimorphism. Many insect species show extreme sexual dimorphism, including beetles with “weapon traits” represented by extremely developed horns and mandibles. Existing studies of sex‐specific development of beetle weapon traits suggest that sex‐specific gene expression plays an important role. On the other hand, contributions of the Y‐chromosome, which may potentially carry genes necessary for male development, to weapon trait expression have not been examined. In holometabolous insects, including beetles, the feminizing gene transformer (<jats:italic>tra</jats:italic>) is roughly conserved in its feminizing function. Only females express a functional isoform of Tra, which causes female differentiation. Knocking down <jats:italic>tra</jats:italic> in females leads to male tissue differentiation, enabling us to analyze male phenotypes in individuals lacking a Y‐chromosome (XX‐males). In this study, we investigate whether the Y‐chromosome is necessary for stag beetles to express male‐specific weapon traits by comparing <jats:italic>tra</jats:italic>‐knockdown‐induced XX‐males with natural XY males. We show that XX‐males could express weapons (enlarged mandibles) as in XY‐males. These results suggest that the Y‐chromosome does not have a major role in weapon trait expression in this species.</jats:p>

DOI： 10.1002/jez.b.23274

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Language：English   Publishing type：Research paper (scientific journal)  

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are now a public health concern in both community and healthcare settings worldwide. We previously identified a suspected case of a maternity clinic-centred outbreak of CA-MRSA skin infection in a regional community in Japan by PFGE-based analysis. In this study, we performed genome sequence-based analyses of 151 CA-MRSA isolates, which included not only outbreak-related isolates that we previously defined based on identical or similar PFGE patterns but also other isolates obtained during the same period in the same region. Our analysis accurately defined 133 isolates as outbreak-related isolates, collectively called the TDC clone. They belonged to a CA-MRSA lineage in clonal complex (CC) 30, known as the South West Pacific (SWP) clone. A high-resolution phylogenetic analysis of these isolates combined with their epidemiological data revealed that the TDC clone was already present and circulating in the region before the outbreak was recognized, and only the isolates belonging to two sublineages (named SL4 and SL5) were directly involved in the outbreak. Long persistence in patients/carriers and frequent intrahousehold transmission of the TDC clone were also revealed by this analysis. Moreover, by systematic analyses of the genome changes that occurred in this CA-MRSA clone during transmission in the community, we revealed that most variations were associated with mobile genetic elements (MGEs). Variant PFGE types were generated by alterations of prophages and genomic islands or insertion sequence (IS)-mediated insertion of a plasmid or a sequence of unknown origin. Dynamic changes in plasmid content, which were linked to changes in antimicrobial resistance profiles in specific isolates, were generated by frequent gain and loss of plasmids, most of which were self-transmissible or mobilizable. The introduction of IS256 by a plasmid (named pTDC02) into sublineage SL5 led to SL5-specific amplification of IS256, and amplified IS256 copies were involved in some of the structural changes of chromosomes and plasmids and generated variations in the repertoire of virulence-related genes in limited isolates. These data revealed how CA-MRSA genomes change during transmission in the community and how MGEs are involved in this process.

DOI： 10.1099/mgen.0.001272

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Language：English   Publishing type：Research paper (scientific journal)  

Allorecognition-the ability of an organism to discriminate between self and nonself-is crucial to colonial marine animals to avoid invasion by other individuals in the same habitat. The cnidarian hydroid Hydractinia has long been a major research model in studying invertebrate allorecognition, establishing a rich knowledge foundation. In this study, we introduce a new cnidarian model Cladonema radiatum (C. radiatum). C. radiatum is a hydroid jellyfish which also forms polyp colonies interconnected with stolons. Allorecognition responses-fusion or regression of stolons-are observed when stolons encounter each other. By transmission electron microscopy, we observe rapid tissue remodeling contributing to gastrovascular system connection in fusion. Meanwhile, rejection responses are regulated by reconstruction of the chitinous exoskeleton perisarc, and induction of necrotic and autophagic cellular responses at cells in contact with the opponent. Genetic analysis identifies allorecognition genes: six Alr genes located on the putative allorecognition complex and four immunoglobulin superfamily genes on a separate genome region. C. radiatum allorecognition genes show notable conservation with the Hydractinia Alr family. Remarkedly, stolon encounter assays of inbred lines reveal that genotypes of Alr1 solely determine allorecognition outcomes in C. radiatum.

DOI： 10.1002/jez.2853

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in four species, including two paedophages, which began during the 1970s–1980s, and population size rebounded during the 1990s-2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines’ disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the four species that likely experienced bottleneck, Haplochromis sp. ‘matumbi hunter,’ a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the five paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.

DOI： 10.1093/molbev/msae093

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Language：English   Publishing type：Research paper (scientific journal)  

INTRODUCTION: X chromosome inactivation (XCI) is an essential mechanism for dosage compensation between females and males in mammals. In females, XCI is controlled by a complex, conserved locus termed the X inactivation center (Xic), in which the lncRNA Xist is the key regulator. However, little is known about the Xic in species with unusual sex chromosomes. The genus Tokudaia includes three rodent species endemic to Japan. Tokudaia osimensis (TOS) and Tokudaia tokunoshimensis (TTO) lost the Y chromosome (XO/XO), while Tokudaia muenninki (TMU) acquired a neo-X region by fusion of the X chromosome and an autosome (XX/XY). We compared the gene location and structure in the Xic among Tokudaia species. METHODS: Gene structure of nine genes in Xic were predicted, and the gene location and genome sequences of Xic were compared between mouse and Tokudaia species. The expression level of gene was confirmed by TPM calculation using RNA-seq data. RESULTS: Compared to mouse, the Xic gene order and location were conserved in Tokudaia species. However, remarkable structure changes were observed in lncRNA genes, Xist and Tsix, in the XO/XO species. In Xist, important functional repeats, B-, C-, D-, and E-repeats, were partially or completely lost due to deletions in these species. RNA-seq data showed that female-specific expression patterns of Xist and Tsix were confirmed in TMU, however not in the XO/XO species. Additionally, three deletions and one inversion were confirmed in the intergenic region between Jpx and Ftx in the XO/XO species. CONCLUSION: Our findings indicate that even if the Xist and Tsix lncRNAs are expressed, they are incapable of producing a successful and lasting XCI in the XO/XO species. We hypothesized that the significant structure change in intergenic region of Jpx-Ftx resulted in the inability to perform the X chromosome inactivation, and, as a result, a lack of Xist expression. Our results collectively suggest that structural changes in the Xic occurred in the ancestral lineage of XO/XO species, likely due to the loss of one X chromosome and the Y chromosome and a consequence of the degradation of XCI system.

DOI： 10.1159/000539294

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.ygcen.2024.114476

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DOI： 10.1016/j.jbiosc.2024.01.006

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DOI： 10.1111/tpj.16764

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<jats:p>SDF-1/CXCR4 chemokine signaling are indispensable for cell migration, especially the Primordial Germ Cell (PGC) migration towards the gonadal ridge during early development. We earlier found that this signaling is largely conserved in the Japanese anchovy (<jats:italic>Engraulis japonicus</jats:italic>, EJ), and a mere treatment of CXCR4 antagonist, AMD3100, leads to germ cell depletion and thereafter gonad sterilization. However, the effect of AMD3100 was limited. So, in this research, we scouted for CXCR4 antagonist with higher potency by employing advanced artificial intelligence deep learning-based computer simulations. Three potential candidates, AMD3465, WZ811, and LY2510924, were selected and <jats:italic>in vivo</jats:italic> validation was conducted using Japanese anchovy embryos. We found that seven transmembrane motif of EJ CXCR4a and EJ CXCR4b were extremely similar with human homolog while the CXCR4 chemokine receptor N terminal (PF12109, essential for SDF-1 binding) was missing in EJ CXCR4b. 3D protein analysis and cavity search predicted the cavity in EJ CXCR4a to be five times larger (6,307 Å³) than that in EJ CXCR4b (1,241 Å³). Docking analysis demonstrated lower binding energy of AMD3100 and AMD3465 to EJ CXCR4a (Vina score −9.6) and EJ CXCR4b (Vina score −8.8), respectively. Furthermore, we observed significant PGC mismigration in microinjected AMD3465 treated groups at 10, 100 and 1 × 10<jats:sup>5</jats:sup> nM concentration in 48 h post fertilized embryos. The other three antagonists showed various degrees of PGC dispersion, but no significant effect compared to their solvent control at tested concentrations was observed. Cumulatively, our results suggests that AMD3645 might be a better candidate for abnormal PGC migration in Japanese anchovy and warrants further investigation.</jats:p>

DOI： 10.3389/fphys.2024.1349119

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DOI： 10.1038/s41597-023-02845-1

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Language：English   Publishing type：Research paper (scientific journal)  

The genomes of obligate bacterial co-symbionts of the green rice leafhopper Nephotettix cincticeps, which is notorious as an agricultural pest, were determined. The streamlined genomes of "Candidatus Sulcia muelleri" and "Candidatus Nasuia deltocephalinicola" exhibited complementary metabolic pathways for synthesizing essential nutrients that contribute to host adaptation.

DOI： 10.1128/MRA.00353-23

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Cephonodes hylas, the coffee bee hawkmoth is a hawkmoth species with unique characteristics, such as larvae feeding on gardenia, overcoming the toxicity of its iridoid glycosides, diurnal adults, and transparent wings. Although C. hylas is a fascinating model for molecular biological research, genome sequence analysis-based genetic approaches to elucidate these peculiarities have not yet been undertaken. We successfully achieved de novo genome assembly at the chromosome level of C. hylas comparable to the Lepidoptera model organism, silkworm. Additionally, 16,854 protein-coding genes were annotated, and the constructed genome sequence and annotated genes were of the highest quality BUSCO completion compared to closely related species. Comparative genome analysis revealed the process of chromosomal evolution from the Bombycoidea ancestral (n = 31) genome and changes in turnover at the chromosome level associated with chromosomal fusion events, such as the rate of repetitive sequence insertion. These analyses were only possible because the genome was constructed at the chromosome level. Additionally, increased the nonsynonymous/synonymous rate (dN/dS) ratios were observed in multiple photoreceptor-related genes that were strongly associated with the acquisition of diurnal activity. Furthermore, tandemly duplicated expanded genes containing many digestive and other enzymes and larval midgut-specific expression were also confirmed. These genes may be involved in the metabolism of genipin, a toxin found in gardenias. Using the genome sequence of C. hylas determined at the chromosome level, we have successfully identified new insights into the chromosomal evolution of Bombycoidea, as well as the relationship between the genome sequence and its characteristic traits.

DOI： 10.1093/gbe/evad141

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The prediction of gene structure within the genome sequence is the starting point of genome analysis, and its accuracy has a significant impact on the quality of subsequent analyses. Gene structure prediction is roughly divided into RNA-Seq-based methods, ab initio-based methods, homology-based methods, and the integration of individual prediction methods. Integrated methods are mainstream in recent genome projects because they improve prediction accuracy by combining or taking the best individual prediction findings; however, adequate prediction accuracy for eukaryotic species has not yet been achieved. Therefore, we developed an integrated tool, GINGER, that solves various issues related to gene structure prediction in higher eukaryotes. By handling artifacts in alignments of RNA and protein sequences, reconstructing gene structures via dynamic programming with appropriately weighted and scored exon/intron/intergenic regions, and applying different prediction processes and filtering criteria to multi-exon and single-exon genes, we achieved a significant improvement in accuracy compared to the existing integration methods. The feature of GINGER is its high prediction accuracy at the gene and exon levels, which is pronounced for species with more complex gene architectures. GINGER is implemented using Nextflow, which allows for the efficient and effective use of computing resources.

DOI： 10.1093/dnares/dsad017

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DOI： 10.1101/2023.07.17.549334

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Chromosome-level haplotype-resolved genome assembly is an important resource in molecular biology. However, current de novo haplotype assemblers require parental data or reference genomes and often fail to provide chromosome-level results. We present GreenHill, a novel scaffolding and phasing tool that considers various assemblers' contigs as input to reconstruct chromosome-level haplotypes using Hi-C without parental or reference data. Its unique functions include new error correction based on Hi-C contacts and the simultaneous use of Hi-C and long reads. Benchmarks reveal that GreenHill outperforms other approaches in contiguity and phasing accuracy, and the majority of chromosome arms are entirely phased.

DOI： 10.1186/s13059-023-03006-8

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In Japan, wasabi (Eutrema japonicum) is an important traditional condiment, and is recognized as an endemic species. In the present study, we generated a chromosome-level and haplotype-resolved reference genome for E. japonicum using PacBio CLR (continuous long reads), Illumina, and Hi-C sequencing data. The genome consists of 28 chromosomes that contain 1,512.1 Mb of sequence data, with a scaffold N50 length of 55.67 Mb. We also reported the subgenome and haplotype assignment of the 28 chromosomes by read-mapping and phylogenic analysis. Three validation methods (Benchmarking Universal Single-Copy Orthologs, Merqury, and Inspector) indicated that our obtained genome sequences were a high-quality and high-completeness genome assembly. Comparison of genome assemblies from previously published genomes showed that our obtained genome was of higher quality. Therefore, our genome will serve as a valuable genetic resource for both chemical ecology and evolution research of the genera Eutrema and Brassicaceae, as well as for wasabi breeding.

DOI： 10.1038/s41597-023-02356-z

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1111/tpj.16311

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Among the nine clades of Shiga toxin (Stx)-producing Escherichia coli O157:H7, clade 8 is thought to be highly pathogenic, as it causes severe disease more often than other clades. Two subclades have been proposed, but there are conflicting reports on intersubclade differences in Stx2 levels, although Stx2 production is a risk factor for severe disease development. The global population structure of clade 8 has also yet to be fully elucidated. Here, we present genome analyses of a global clade 8 strain set (n=510), including 147 Japanese strains sequenced in this study. The complete genome sequences of 18 of the 147 strains were determined to perform detailed clade-wide genome analyses together with 17 publicly available closed genomes. Intraclade variations in Stx2 production level and disease severity were also re-evaluated within the phylogenetic context. Based on phylogenomic analysis, clade 8 was divided into four lineages corresponding to the previously proposed SNP genotypes (SGs): SG8_30, SG8_31A, SG8_31B and SG8_32. SG8_30 and the common ancestor of the other SGs were first separated, with SG8_31A and SG8_31B emerging from the latter and SG8_32 emerging from SG8_31B. Comparison of 35 closed genomes revealed the overall structure of chromosomes and pO157 virulence plasmids and the prophage contents to be well conserved. However, Stx2a phages exhibit notable genomic diversity, even though all are integrated into the argW locus, indicating that subtype changes in Stx2a phage occurred from the γ subtype to its variant (γ_v1) in SG8_31A and from γ to δ in SG8_31B and SG8_32 via replacement of parts or almost entire phage genomes, respectively. We further show that SG8_30 strains (all carrying γ Stx2a phages) produce significantly higher levels of Stx2 and cause severe disease more frequently than SG8_32 strains (all carrying δ Stx2a phages). Clear conclusions on SG8_31A and SG8_31B cannot be made due to the small number of strains available, but as SG8_31A (carrying γ_v1 Stx2a phages) contains strains that produce much more Stx2 than SG8_30 strains, attention should also be paid to this SG.

DOI： 10.1099/mgen.0.000935

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Polyhydroxyalkanoate (PHA) is a type of biopolymer produced by most bacteria and archaea, resembling thermoplastic with biodegradability and biocompatibility features. Here, we report the complete genome of a PHA producer, Aquitalea sp. USM4, isolated from Perak, Malaysia. This bacterium possessed a 4.2 Mb circular chromosome and a 54,370 bp plasmid. A total of 4067 predicted protein-coding sequences, 87 tRNA genes, and 25 rRNA operons were identified using PGAP. Based on ANI and dDDH analysis, the Aquitalea sp. USM4 is highly similar to Aquitalea pelogenes. We also identified genes, including acetyl-CoA (phaA), acetoacetyl-CoA (phaB), PHA synthase (phaC), enoyl-CoA hydratase (phaJ), and phasin (phaP), which play an important role in PHA production in Aquitalea sp. USM4. The heterologous expression of phaC1 from Aquitalea sp. USM4 in Cupriavidus necator PHB-4 was able to incorporate six different types of PHA monomers, which are 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), 4-hydroxybutyrate (4HB), 5-hydroxyvalerate (5HV), 3-hydroxyhexanoate (3HHx) and isocaproic acid (3H4MV) with suitable precursor substrates. This is the first complete genome sequence of the genus Aquitalea among the 22 genome sequences from 4 Aquitalea species listed in the GOLD database, which provides an insight into its genome evolution and molecular machinery responsible for PHA biosynthesis.

DOI： 10.1007/s00203-023-03406-1

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In the Japanese hagfish, Eptatretus burgeri, approximately 21% of the genomic DNA in germ cells (2n = 52) consists of 16 chromosomes (eliminated [E]-chromosomes) that are eliminated from presumptive somatic cells (2n = 36). To uncover the eliminated genome (E-genome), we have identified 16 eliminated repetitive DNA families from eight hagfish species, with 11 of these repeats being selectively amplified in the germline genome of E. burgeri. Furthermore, we have demonstrated that six of these sequences, namely EEEb1-6, are exclusively localized on all 16 E-chromosomes. This has led to the hypothesis that the eight pairs of E-chromosomes are derived from one pair of ancestral chromosomes via multiple duplication events over a prolonged evolutionary period. NGS analysis has recently facilitated the re-assembly of two distinct draft genomes of E. burgeri, derived from the testis and liver. This advancement allows for the prediction of not only nonrepetitive eliminated sequences but also over 100 repetitive and eliminated sequences, accomplished through K-mer-based analysis. In this study, we report four novel eliminated repetitive DNA sequences (designated as EEEb7-10) and confirm the relative chromosomal localization of all eliminated repeats (EEEb1-10) by fluorescence in situ hybridization (FISH). With the exception of EEEb10, all sequences were exclusively detected on EEEb1-positive chromosomes. Surprisingly, EEEb10 was detected as an intense signal on EEEb1-positive chromosomes and as a scattered signal on other chromosomes in germ cells. The study further divided the eight pairs of E-chromosomes into six groups based on the signal distribution of each DNA family, and fiber-FISH experiments showed that the EEEb2-10 family was dispersed in the EEEb1-positive extended chromatin fiber. These findings provide new insights into the mechanisms underlying chromosome elimination and the evolution of E-chromosomes, supporting our previous hypothesis.

DOI： 10.1371/journal.pone.0286941

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Mammalian sex chromosomes are highly conserved, and sex is determined by SRY on the Y chromosome. Two exceptional rodent groups in which some species lack a Y chromosome and Sry offer insights into how novel sex genes can arise and replace Sry, leading to sex chromosome turnover. However, intensive study over three decades has failed to reveal the identity of novel sex genes in either of these lineages. We here report our discovery of a male-specific duplication of an enhancer of Sox9 in the Amami spiny rat Tokudaia osimensis, in which males and females have only a single X chromosome (XO/XO) and the Y chromosome and Sry are completely lost. We performed a comprehensive survey to detect sex-specific genomic regions in the spiny rat. Sex-related genomic differences were limited to a male-specific duplication of a 17-kb unit located 430 kb upstream of Sox9 on an autosome. Hi-C analysis using male spiny rat cells showed the duplicated region has potential chromatin interaction with Sox9. The duplicated unit harbored a 1,262-bp element homologous to mouse enhancer 14 (Enh14), a candidate Sox9 enhancer that is functionally redundant in mice. Transgenic reporter mice showed that the spiny rat Enh14 can function as an embryonic testis enhancer in mice. Embryonic gonads of XX mice in which Enh14 was replaced by the duplicated spiny rat Enh14 showed increased Sox9 expression and decreased Foxl2 expression. We propose that male-specific duplication of this Sox9 enhancer substituted for Sry function, defining a novel Y chromosome in the spiny rat.

DOI： 10.1073/pnas.2211574119

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The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of A. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.

DOI： 10.1093/gbe/evac140

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DOI： 10.1098/rstb.2021.0198

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Alternative splicing underpins functional diversity in proteins and the complexity and diversity of eukaryotes. An example is the doublesex gene, the key transcriptional factor in arthropod sexual differentiation. doublesex is controlled by sex-specific splicing and promotes both male and female differentiation in holometabolan insects, whereas in hemimetabolan species, doublesex has sex-specific isoforms but is not required for female differentiation. How doublesex evolved to be essential for female development remains largely unknown. Here, we investigate ancestral states of doublesex using Thermobia domestica belonging to Zygentoma, the sister group of Pterygota, that is, winged insects. We find that, in T. domestica, doublesex expresses sex-specific isoforms but is only necessary for male differentiation of sexual morphology. This result supports the hypothesis that doublesex initially promoted male differentiation during insect evolution. However, T. domestica doublesex has a short female-specific region and upregulates the expression of vitellogenin homologs in females, suggesting that doublesex may already play some role in female morphogenesis of the common ancestor of Pterygota. Reconstruction of the ancestral sequence and prediction of protein structures show that the female-specific isoform of doublesex has an extended C-terminal disordered region in holometabolan insects but not in nonholometabolan species. We propose that doublesex acquired its function in female morphogenesis through a change in the protein motif structure rather than the emergence of the female-specific exon.

DOI： 10.1093/molbev/msac145

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Language：English   Publishing type：Research paper (scientific journal)  

Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.

DOI： 10.1093/dnares/dsac019

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Language：English   Publishing type：Research paper (scientific journal)  

Beyond their well-known role in respiration, mitochondria of land plants contain biologically essential and/or agriculturally important genes whose function and regulation are not fully understood. Until recently, it has been difficult to analyze these genes or, in the case of crops, to improve their functions, due to a lack of methods for stably modifying plant mitochondrial genomes. In rice, rapeseed, and Arabidopsis thaliana, mitochondria-targeting transcription activator-like effector nucleases (mitoTALENs) have recently been used to disrupt targeted genes in an inheritable and stable manner. However, this technique can also induce large deletions around the targeted sites, as well as cause ectopic homologous recombinations, which can change the sequences and gene order of mitochondrial genomes. Here, we used mitochondria-targeting TALEN-based cytidine deaminase to successfully substitute targeted C:G pairs with T:A pairs in the mitochondrial genomes of plantlets of A. thaliana without causing deletions or changes in genome structure. Expression vectors of the base editor genes were stably introduced into the nuclear genome by the easy-to-use floral dipping method. Some T1 plants had apparent homoplasmic substitutions that were stably inherited by seed progenies, independently of the inheritance of nuclear-introduced genes. As a demonstration of the method, we used it to restore the growth of an organelle transcript processing 87 (otp87) mutant that is defective in the editing of RNA transcripts of the mitochondrial atp1 gene and to identify bases in atp1 that affect the efficiency of RNA editing by OTP87.

DOI： 10.1073/pnas.2121177119

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Language：English   Publishing type：Research paper (scientific journal)  

Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.

DOI： 10.1099/mgen.0.000793

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Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media {SA}  

<jats:p>The estimation of larval dispersal on an ecological timescale is significant for conservation of marine species. In 2018, a semi-population outbreak of crown-of-thorns sea star, <jats:italic>Acanthaster</jats:italic> cf. <jats:italic>solaris</jats:italic>, was observed on a relatively isolated oceanic island, Ogasawara. The aim of this study was to assess whether this population outbreak was caused by large-scale larval recruitment (termed secondary outbreak) from the Kuroshio region. We estimated larval dispersal of the coral predator <jats:italic>A.</jats:italic> cf. <jats:italic>solaris</jats:italic> between the Kuroshio and Ogasawara regions using both population genomic analysis and simulation of oceanographic dispersal. Population genomic analysis revealed overall genetically homogenized patterns among Ogasawara and other Japanese populations, suggesting that the origin of the populations in the two regions is the same. In contrast, a simulation of 26-year oceanographic dispersal indicated that larvae are mostly self-seeded in Ogasawara populations and have difficulty reaching Ogasawara from the Kuroshio region within one generation. However, a connectivity matrix produced by the larval dispersal simulation assuming a Markov chain indicated gradual larval dispersal migration from the Kuroshio region to Ogasawara in a stepping-stone manner over multiple years. These results suggest that the 2018 outbreak was likely the result of self-seeding, including possible inbreeding (as evidenced by clonemate analysis), as large-scale larval dispersal from the Kurishio population to the Ogasawara population within one generation is unlikely. Instead, the population in Ogasawara is basically sustained by self-seedings, and the outbreak in 2018 was also most likely caused by successful self-seedings including possible inbreeding, as evidenced by clonemate analysis. This study also highlighted the importance of using both genomic and oceanographic methods to estimate larval dispersal, which provides significant insight into larval dispersal that occurs on ecological and evolutionary timescales.</jats:p>

DOI： 10.3389/fmars.2021.688139

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Language：English   Publishing type：Research paper (scientific journal)  

Bacterial small RNAs regulate the expression of multiple genes through imperfect base-pairing with target mRNAs mediated by RNA chaperone proteins such as Hfq. GcvB is the master sRNA regulator of amino acid metabolism and transport in a wide range of Gram-negative bacteria. Recently, independent RNA-seq approaches identified a plethora of transcripts interacting with GcvB in Escherichia coli. In this study, the compilation of RIL-seq, CLASH, and MAPS data sets allowed us to identify GcvB targets with high accuracy. We validated 21 new GcvB targets repressed at the posttranscriptional level, raising the number of direct targets to >50 genes in E. coli. Among its multiple seed sequences, GcvB utilizes either R1 or R3 to regulate most of these targets. Furthermore, we demonstrated that both R1 and R3 seed sequences are required to fully repress the expression of gdhA, cstA, and sucC genes. In contrast, the ilvLXGMEDA polycistronic mRNA is targeted by GcvB through at least four individual binding sites in the mRNA. Finally, we revealed that GcvB is involved in the susceptibility of peptidase-deficient E. coli strain (Δpeps) to Ala-Gln dipeptide by regulating both Dpp dipeptide importer and YdeE dipeptide exporter via R1 and R3 seed sequences, respectively.

DOI： 10.1111/mmi.14814

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Publishing type：Research paper (scientific journal)  

DOI： 10.1099/mgen.0.000716

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Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

DOI： 10.1093/nar/gkab831

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DOI： 10.1038/s42003-021-02704-y

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Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

Abstract

Birds in the clade Palaeognathae, excluding Tinamiformes, have morphologically conserved karyotypes and less differentiated ZW sex chromosomes compared with those of other birds. In particular, the sex chromosomes of the ostrich and emu have exceptionally large recombining pseudoautosomal regions (PARs), whereas non-PARs are classified into two strata according to the date of their origins: stratum 0 and stratum 1 (S1). However, the construction and analysis of the genome sequences in these regions in the clade Palaeognathae can be challenging because assembling the S1 region is difficult owing to low sequence diversity between gametologs (Z-linked and W-linked sequences). We addressed this issue by applying the Platanus-allee assembler and successfully constructed the haplotype-resolved (phased) assembly for female emu, cassowary, and ostrich using only sequence read data derived from the Illumina platform. Comparative genomic and phylogenetic analyses based on assembled Z-linked and W-linked sequences confirmed that the S1 region of emu and cassowary formed in their common ancestor. Moreover, the interspersed repetitive sequence landscapes in the S1 regions of female emu showed an expansion of younger repetitive elements in the W-linked S1 region, suggesting an interruption in homologous recombination in the S1 region. These results provide novel insights into the trajectory of sex chromosome evolution in the clade Palaeognathae and suggest that the Illumina-based phased assembly method is an effective approach for elucidating the evolutionary process underlying the transition from homomorphic to differentiated sex chromosomes.

DOI： 10.1093/gbe/evab242

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Other Link： https://academic.oup.com/gbe/article-pdf/13/11/evab242/41162093/evab242.pdf

Language：English   Publishing type：Research paper (scientific journal)  

The crown-of-thorns starfish (COTS) is a coral predator that is widely distributed in Indo-Pacific Oceans. A previous phylogenetic study using partial mitochondrial sequences suggested that COTS had diverged into four distinct species, but a nuclear genome-based analysis to confirm this was not conducted. To address this, COTS species nuclear genome sequences were analysed here, sequencing Northern Indian Ocean (NIO) and Red Sea (RS) species genomes for the first time, followed by a comparative analysis with the Pacific Ocean (PO) species. Phylogenetic analysis and ADMIXTURE analysis revealed clear divergences between the three COTS species. Furthermore, within the PO species, the phylogenetic position of the Hawaiian sample was further away from the other Pacific-derived samples than expected based on the mitochondrial data, suggesting that it may be a PO subspecies. The pairwise sequentially Markovian coalescent model showed that the trajectories of the population size diverged by region during the Mid-Pleistocene transition when the sea-level was dramatically decreased, strongly suggesting that the three COTS species experienced allopatric speciation. Analysis of the orthologues indicated that there were remarkable genes with species-specific positive selection in the genomes of the PO and RS species, which suggested that there may be local adaptations in the COTS species.

DOI： 10.1093/dnares/dsab012

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s00294-021-01201-3

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Other Link： https://link.springer.com/article/10.1007/s00294-021-01201-3/fulltext.html

Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

DOI： 10.1038/s41477-021-00954-6

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Publisher：Cold Spring Harbor Laboratory  

<title>Abstract</title>Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (<italic>Chrysanthemum seticuspe</italic>), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the <italic>C. seticuspe</italic> genome. The genome contained more than 80% interspread repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in <italic>C. seticuspe</italic>, contributing to a relatively large genome size. Furthermore, we identified aretrotransposon, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in <italic>C. seticuspe</italic>. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

DOI： 10.1101/2021.06.28.450068

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Language：English   Publishing type：Research paper (scientific journal)  

The spatial organization of chromatin is known to be highly dynamic in response to environmental stress. However, it remains unknown how chromatin dynamics contributes to or modulates disease pathogenesis. Here, we show that upon influenza virus infection, the H4K20me3 methyltransferase Suv4-20h2 binds the viral protein NP, which results in the inactivation of Suv4-20h2 and the dissociation of cohesin from Suv4-20h2. Inactivation of Suv4-20h2 by viral infection or genetic deletion allows the formation of an active chromatin loop at the HoxC8-HoxC6 loci coincident with cohesin loading. HoxC8 and HoxC6 proteins in turn enhance viral replication by inhibiting the Wnt-β-catenin mediated interferon response. Importantly, loss of Suv4-20h2 augments the pathology of influenza infection in vivo. Thus, Suv4-20h2 acts as a safeguard against influenza virus infection by suppressing cohesin-mediated loop formation.

DOI： 10.1016/j.isci.2021.102660

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1093/dnares/dsab004

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Publishing type：Research paper (scientific journal)  

DOI： 10.26508/LSA.202000905

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Language：English   Publishing type：Research paper (scientific journal)  

The greater argonaut Argonauta argo is a species of the paper nautilus (Argonautidae), which is a family in Octopoda. In this paper, we report its full mitogenome sequence, which was obtained from a specimen collected in the Japan Seas near Oki Island, Shimane Prefecture, in Japan. The sequence was determined using the NGS Illumina HiSeq platform. With its 37 genes, the mitogenome shows a typical metazoan and Octopoda genomic structure, and similar to the mitogenome of the previously reported congener, A. hians. To confirm A. argo phylogenetic position in Octopoda, we conducted maximum likelihood phylogenetic analysis, using a data set including publicly available 17 Octopodiformes, five Decapodiformes, three Nautiloids and two outgroup Conchiferans. The result confirmed the affinity of Argonautidae to Tremoctopus, and the sister group position of this clade against the rest of incirrate Octopods. The mitogenome and phylogeny of A. argo reported here will be useful for future studies involving this enigmatic species, including on the reacquisition of external calcified shell structures in mollusks.

DOI： 10.1080/23802359.2021.1911710

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

<jats:title>Abstract</jats:title>
<jats:p>The cichlids of Lake Victoria are a textbook example of adaptive radiation, as &amp;gt;500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments—Haplochromis chilotes, H. sauvagei, and Lithochromis rufus—to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.</jats:p>

DOI： 10.1093/molbev/msab084

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

<jats:title>Abstract</jats:title>
<jats:p>In animal gonads, transposable elements are actively repressed to preserve genome integrity through the PIWI-interacting RNA (piRNA) pathway. In mice, piRNAs are abundantly expressed in male germ cells, and form effector complexes with three distinct PIWIs. The depletion of individual Piwi genes causes male-specific sterility with no discernible phenotype in female mice. Unlike mice, most other mammals have four PIWI genes, some of which are expressed in the ovary. Here, purification of PIWI complexes from oocytes of the golden hamster revealed that the size of the PIWIL1-associated piRNAs changed during oocyte maturation. In contrast, PIWIL3, an ovary-specific PIWI in most mammals, associates with short piRNAs only in metaphase II oocytes, which coincides with intense phosphorylation of the protein. An improved high-quality genome assembly and annotation revealed that PIWIL1- and PIWIL3-associated piRNAs appear to share the 5′-ends of common piRNA precursors and are mostly derived from unannotated sequences with a diminished contribution from TE-derived sequences, most of which correspond to endogenous retroviruses. Our findings show the complex and dynamic nature of biogenesis of piRNAs in hamster oocytes, and together with the new genome sequence generated, serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes.</jats:p>

DOI： 10.1093/nar/gkab059

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

<jats:title>Abstract</jats:title><jats:p>Mussels, which occupy important positions in marine ecosystems, attach tightly to underwater substrates using a proteinaceous holdfast known as the byssus, which is tough, durable, and resistant to enzymatic degradation. Although various byssal proteins have been identified, the mechanisms by which it achieves such durability are unknown. Here we report comprehensive identification of genes involved in byssus formation through whole-genome and foot-specific transcriptomic analyses of the green mussel, <jats:italic>Perna viridis</jats:italic>. Interestingly, proteins encoded by highly expressed genes include proteinase inhibitors and defense proteins, including lysozyme and lectins, in addition to structural proteins and protein modification enzymes that probably catalyze polymerization and insolubilization. This assemblage of structural and protective molecules constitutes a multi-pronged strategy to render the byssus highly resistant to environmental insults.</jats:p>

DOI： 10.1038/s41598-021-84948-6

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Language：Japanese   Publisher：日本比較内分泌学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

DOI： 10.1186/s40168-020-00880-3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1111/tpj.15041

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

<jats:title>Abstract</jats:title><jats:p>Research on avian sex determination has focused on the chicken. In this study, we established the utility of another widely used animal model, the Japanese quail (<jats:italic>Coturnix japonica</jats:italic>), for clarifying the molecular mechanisms underlying gonadal sex differentiation. In particular, we performed comprehensive gene expression profiling of embryonic gonads at three stages (HH27, HH31 and HH38) by mRNA-seq. We classified the expression patterns of 4,815 genes into nine clusters according to the extent of change between stages. Cluster 2 (characterized by an initial increase and steady levels thereafter), including 495 and 310 genes expressed in males and females, respectively, contained five key genes involved in gonadal sex differentiation. A GO analysis showed that genes in this cluster are related to developmental processes including reproductive structure development and developmental processes involved in reproduction were significant, suggesting that expression profiling is an effective approach to identify novel candidate genes. Based on RNA-seq data and in situ hybridization, the expression patterns and localization of most key genes for gonadal sex differentiation corresponded well to those of the chicken. Our results support the effectiveness of the Japanese quail as a model for studies gonadal sex differentiation in birds.</jats:p>

DOI： 10.1038/s41598-020-77094-y

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

<jats:title>ABSTRACT</jats:title>
<jats:p>The draft genome sequence of the deep-sea yeast <jats:italic>Naganishia liquefaciens</jats:italic> strain N6, isolated from the Japan Trench, is reported here. This strain was previously classified into a <jats:italic>Cryptococcus</jats:italic> clade. Phylogenetic analysis using the presented sequence suggests that strain N6 is in the clade of the genus <jats:italic>Naganishia</jats:italic>.</jats:p>

DOI： 10.1128/mra.00827-20

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41396-020-0688-1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1111/dgd.12689

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Publishing type：Research paper (scientific journal)  

DOI： 10.1101/2020.07.07.191841

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

<jats:title>Abstract</jats:title>
<jats:p>De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.</jats:p>

DOI： 10.1093/dnares/dsaa014

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Publisher：Cold Spring Harbor Laboratory  

Abstract

Like animals, plants accommodate a rich diversity of microbes, typically without discernible disease symptoms. How their pathogenesis is prevented in the host remains obscure. Here, we show that the root-infecting fungus Colletotrichum fructicola of the C. gloeosporioides clade (CgE), isolated from field-grown healthy Brassicaceae plants, inhibits growth of pathogenic fungi in Arabidopsis thaliana, in a phosphate status-dependent manner. Loss of host ethylene signaling or phytoalexins, camalexin or indole glucosinolates, however, allows CgE to display pathogenesis, suggesting host contributions to endophytic CgE colonization and benefit. Compared to a closely-related C. gloeosporioides pathogen (CgP), CgE is characterized by genome expansion and &gt;700 fungal genes (4.34%) specifically induced in the host roots when co-inoculated with CgP, including genes related to fungal secondary metabolism. This may underlie antimicrobial tolerance of CgE and its dominance over pathogenic fungi within the host, pointing to a role for fungus-fungus competition in asymptomatic fungal colonization in plants.

DOI： 10.1101/2020.05.27.117978

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Publishing type：Research paper (scientific journal)   Publisher：Microbiology Society  

DOI： 10.1099/mgen.0.000323

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Nature Research  

DOI： 10.1038/s42003-019-0592-2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

<jats:title>Abstract</jats:title>
<jats:p>In bacterial genome and metagenome sequencing, Illumina sequencers are most frequently used due to their high throughput capacity, and multiple library preparation kits have been developed for Illumina platforms. Here, we systematically analysed and compared the sequencing bias generated by currently available library preparation kits for Illumina sequencing. Our analyses revealed that a strong sequencing bias is introduced in low-GC regions by the Nextera XT kit. The level of bias introduced is dependent on the level of GC content; stronger bias is generated as the GC content decreases. Other analysed kits did not introduce this strong sequencing bias. The GC content-associated sequencing bias introduced by Nextera XT was more remarkable in metagenome sequencing of a mock bacterial community and seriously affected estimation of the relative abundance of low-GC species. The results of our analyses highlight the importance of selecting proper library preparation kits according to the purposes and targets of sequencing, particularly in metagenome sequencing, where a wide range of microbial species with various degrees of GC content is present. Our data also indicate that special attention should be paid to which library preparation kit was used when analysing and interpreting publicly available metagenomic data.</jats:p>

DOI： 10.1093/dnares/dsz017

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

DOI： 10.1038/s42003-019-0536-x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

DOI： 10.1038/s41477-019-0459-z

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press ({OUP})  

<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Background</jats:title>
<jats:p>Recurrent infections of Helicobacter cinaedi are often reported, and long-term antimicrobial treatment is empirically recommended to prevent such infections. However, there have been no studies examining whether recurrent infections are relapses of former infections or reinfections with different clones.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Methods</jats:title>
<jats:p>A 69-year-old woman presented with recurrent H cinaedi bacteremia-associated cellulitis after a 51-day interval. We isolated 10 colonies from the blood cultures obtained during each of the 2 episodes and subjected them to whole-genome sequencing (WGS). High-confidence single-nucleotide polymorphisms (SNPs) were identified by an assembly based method. Heterogeneous SNP sites were identified by read mapping. The susceptibility of a representative isolate to 14 antimicrobials was also examined.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>Whole-genome sequence analysis revealed only 6 SNP sites among the 20 isolates at the whole-genome level. Based on the 6 SNPs, 5 within-host variants (referred to as genotypes) were identified. All 5 genotypes were detected in the first infection; however, only 2 genotypes were detected in the second infection. Although the H cinaedi clone showed a higher minimum inhibitory concentration to fluoroquinolones and macrolides and responsible mutations were identified, none of the 6 SNPs appeared related to additional resistance.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Conclusions</jats:title>
<jats:p>The second infection analyzed here was a relapse of the first infection. A certain level of within-host genomic heterogeneity of the H cinaedi clone was already present in the first infection. Our results suggest the importance of longer treatment courses to eradicate H cinaedi for preventing the relapse of its infection.</jats:p>
</jats:sec>

DOI： 10.1093/ofid/ofz200

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Microbiology Society  

DOI： 10.1099/mgen.0.000261

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

DOI： 10.1038/s41467-019-09575-2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Rockefeller University Press  

<jats:p>The centromere is an important genomic locus for chromosomal segregation. Although the centromere is specified by sequence-independent epigenetic mechanisms in most organisms, it is usually composed of highly repetitive sequences, which associate with heterochromatin. We have previously generated various chicken DT40 cell lines containing differently positioned neocentromeres, which do not contain repetitive sequences and do not associate with heterochromatin. In this study, we performed systematic 4C analysis using three cell lines containing differently positioned neocentromeres to identify neocentromere-associated regions at the 3D level. This analysis reveals that these neocentromeres commonly associate with specific heterochromatin-rich regions, which were distantly located from neocentromeres. In addition, we demonstrate that centromeric chromatin adopts a compact structure, and centromere clustering also occurs in vertebrate interphase nuclei. Interestingly, the occurrence of centromere–heterochromatin associations depend on CENP-H, but not CENP-C. Our analyses provide an insight into understanding the 3D architecture of the genome, including the centromeres.</jats:p>

DOI： 10.1083/jcb.201805003

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Microbiology Society  

DOI： 10.1099/mgen.0.000236

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Language：English   Publishing type：Research paper (scientific journal)  

Among Shiga toxin (Stx)-producing Escherichia coli (STEC) O157:H7 strains, those producing Stx2a cause more severe diseases. Atypical STEC O157:H7 strains showing a β-glucuronidase-positive phenotype (GP STEC O157:H7) have rarely been isolated from humans, mostly from persons with asymptomatic or mild infections; Stx2a-producing strains have not been reported. We isolated, from a patient with bloody diarrhea, a GP STEC O157:H7 strain (PV15-279) that produces Stx2a in addition to Stx1a and Stx2c. Genomic comparison with other STEC O157 strains revealed that PV15-279 recently emerged from the stx1a/stx2c-positive GP STEC O157:H7 clone circulating in Japan. Major virulence genes are shared between typical (β-glucuronidase-negative) and GP STEC O157:H7 strains, and the Stx2-producing ability of PV15-279 is comparable to that of typical STEC O157:H7 strains; therefore, PV15-279 presents a virulence potential similar to that of typical STEC O157:H7. This study reveals the importance of GP O157:H7 as a source of highly pathogenic STEC clones.

DOI： 10.3201/eid2412.180404

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Language：English   Publishing type：Research paper (scientific journal)  

How genetic information is modified to generate phenotypic variation within a species is one of the central questions in evolutionary biology. Here we focus on the striking intraspecific diversity of >200 aposematic elytral (forewing) colour patterns of the multicoloured Asian ladybird beetle, Harmonia axyridis, which is regulated by a tightly linked genetic locus h. Our loss-of-function analyses, genetic association studies, de novo genome assemblies, and gene expression data reveal that the GATA transcription factor gene pannier is the major regulatory gene located at the h locus, and suggest that repeated inversions and cis-regulatory modifications at pannier led to the expansion of colour pattern variation in H. axyridis. Moreover, we show that the colour-patterning function of pannier is conserved in the seven-spotted ladybird beetle, Coccinella septempunctata, suggesting that H. axyridis' extraordinary intraspecific variation may have arisen from ancient modifications in conserved elytral colour-patterning mechanisms in ladybird beetles.

DOI： 10.1038/s41467-018-06116-1

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DOI： 10.1093/molbev/msy186

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Ovarian clear cell carcinoma (OCCC) is a chemotherapy‑resistant epithelial ovarian cancer with poor prognosis. To identify genomic alterations involved in the development of OCCC, we analyzed somatic copy number alterations in OCCC using comparative genomic hybridization (CGH). Here we showed that the chromosomal regions 8p11.21, 8p11.22, 12p13.31 and 20q13.2 were amplified in OCCC. We also demonstrated that small segments in the chromosomal regions 3q26.1, 4q13.2 and 22q11.23 were deleted. Kaplan‑Meier survival analyses revealed that patients with amplification within 8p11.21 or a deletion within 3q26.1 had a shorter progression‑free survival (PFS) time than those without such alterations. In addition, patients with amplification in three of the four chromosomal regions 8p11.21, 8p11.22, 12p13.31 and 20q13.2 had shorter overall survival (OS). We also demonstrated that amplification of 12p13.3 or three of the four chromosomal regions 8p11.21, 8p11.22, 12p13.31 and 20q13.2, or a deletion in the chromosomal region 3q26.1 was associated with chemotherapy resistance. Our findings suggest that copy number alterations in 8p11.21‑22, 12p13.31, 20q13.2, 3q26.1, 4q13.2 and 22q11.23 are critical for the development and survival of OCCC.

DOI： 10.3892/or.2018.6419

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DOI： 10.1126/sciadv.aao5416

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biomedical Research Foundation  

DOI： 10.2220/biomedres.39.75

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A key virulence factor of enterohaemorrhagic Escherichia coli (EHEC) is the bacteriophage-encoded Shiga toxin (Stx). Stxs are classified into two types, Stx1 and Stx2, and Stx2-producing strains are thought to cause more severe infections than strains producing only Stx1. Although O26 : H11 is the second most prevalent EHEC following O157 : H7, the majority of O26 : H11 strains produce Stx1 alone. However, Stx2-producing O26 strains have increasingly been detected worldwide. Through a large-scale genome analysis, we present a global phylogenetic overview and evolutionary timescale for E. coli O26 : H11. The origin of O26 has been estimated to be 415 years ago. Sequence type 21C1 (ST21C1), one of the two sublineages of ST21, the most predominant O26 : H11 lineage worldwide, emerged 213 years ago from one of the three ST29 sublineages (ST29C2). The other ST21 lineage (ST21C2) emerged 95 years ago from ST21C1. Increases in population size occurred in the late 20th century for all of the O26 lineages, but most remarkably for ST21C2. Analysis of the distribution of stx2-positive strains revealed the recent and repeated acquisition of the stx2 gene in multiple lineages of O26, both in ST21 and ST29. Other major EHEC virulence genes, such as type III secretion system effector genes and plasmid-encoded virulence genes, were well conserved in ST21 compared to ST29. In addition, more antimicrobial-resistance genes have accumulated in the ST21C1 lineage. Although current attention is focused on several highly virulent ST29 clones that have acquired the stx2 gene, there is also a considerable risk that the ST21 lineage could yield highly virulent clones.

DOI： 10.1099/mgen.0.000141

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DOI： 10.1093/dnares/dsw055

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DOI： 10.1038/ismej.2016.191

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DOI： 10.1093/gbe/evw304

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DOI： 10.1264/jsme2.ME16175

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DOI： 10.1038/srep39545

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DOI： 10.1093/gbe/evw227

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DOI： 10.1038/ng.3495

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DOI： 10.1038/ncomms13295

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DOI： 10.1074/jbc.M115.684233

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DOI： 10.1038/nature15366

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DOI： 10.1093/dnares/dsv037

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DOI： 10.1186/s12864-015-1278-x

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DOI： 10.1093/dnares/dsv032

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DOI： 10.1038/ng.3241

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DOI： 10.1242/dev.099150

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DOI： 10.1101/gr.170720.113

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DOI： 10.3389/fmicb.2014.00080

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DOI： 10.1016/j.devcel.2013.10.024

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DOI： 10.1111/gtc.12058

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DOI： 10.1016/j.parint.2012.09.006

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DOI： 10.1101/gr.158105.113

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DOI： 10.1016/j.molcel.2012.01.007

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DOI： 10.1038/nature11316

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DOI： 10.1371/journal.pone.0030559

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DOI： 10.1091/mbc.E10-08-0668

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DOI： 10.1038/nature09791

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DOI： 10.1093/dnares/dsr009

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DOI： 10.1038/emboj.2010.315

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DOI： 10.1016/j.cub.2010.12.004

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DOI： 10.1093/dnares/dsr022

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DOI： 10.1111/j.1365-2672.2011.05089.x

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DOI： 10.1016/j.cub.2010.09.006

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DOI： 10.1038/embor.2010.169

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DOI： 10.1093/nar/gkq346

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DOI： 10.1371/journal.pbio.1000119

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DOI： 10.1016/j.cub.2009.01.062

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DOI： 10.1111/j.1365-2443.2009.01310.x

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DOI： 10.1091/mbc.E08-12-1223

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DOI： 10.1371/journal.ppat.1000408

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DOI： 10.1074/jbc.M109.065730

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DOI： 10.1038/emboj.2008.215

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DOI： 10.1038/nature06634

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DOI： 10.1101/gad.1675708

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DOI： 10.1371/journal.pbio.0060326

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DOI： 10.1038/sj.emboj.7601585

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DOI： 10.1266/ggs.82.517

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DOI： 10.1093/dnares/dsm018

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DOI： 10.1038/sj.emboj.7601708

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DOI： 10.11517/pjsai.JSAI06.0.284.0

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DOI： 10.1038/ng0806-854

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DOI： 10.1016/j.molcel.2006.05.014

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DOI： 10.1083/jcb.200605074

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DOI： 10.1038/nature04664

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DOI： 10.1038/ng1729

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DOI： 10.1038/nature04632

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DOI： 10.1038/nature04363

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DOI： 10.14848/esj.ESJ52.0.135.0

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DOI： 10.1038/ng1648

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DOI： 10.1038/nature03983

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DOI： 10.1038/nature02742

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DOI： 10.1101/sqb.2003.68.455

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DOI： 10.4052/tigg.14.189

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DOI： 10.1126/science.1065199

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DOI： 10.1093/nar/30.1.294

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Macmillan Magazines Ltd  

DOI： 10.1038/35087627

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DOI： 10.1038/35057062

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Other Link： https://www.nature.com/articles/35057062

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DOI： 10.1007/s00335-001-0005-x

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Language：Japanese   Publisher：(株)メディカルドゥ  

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Language：Japanese   Publisher：(株)羊土社  

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Language：Japanese   Publisher：日本ビフィズス菌センター  

メタゲノム解析は培養ステップを経ないで自然環境下に棲息する細菌集団(叢)のゲノム塩基配列を直接決定し，情報学的解析からその細菌叢がもつ生体システムを解明する新たなゲノム解析手法である．これにより，従来では解析困難であった難培養性細菌が大部分を占めるさまざまな環境細菌叢の機能実体を包括的に知ることが可能となった．著者らはメタゲノム解析手法を用いてヒト腸内細菌叢の解析を行った．<br>

DOI： 10.11209/jim.21.187

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Other Link： http://search.jamas.or.jp/link/ui/2008006596

DOI： 10.1038/ng0306-389c

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DOI： 10.11517/pjsai.JSAI05.0.147.0

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