1. A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species.

    PLoS Genetics 11(7):e1005361 (2015) PMID 26172569 PMCID PMC4501782

    Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation. Yet, growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology. ...
  2. Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis.

    PLoS Genetics 11(4):e1005154 (2015) PMID 25902052 PMCID PMC4406451

    Epigenetic variations of phenotypes, especially those associated with DNA methylation, are often inherited over multiple generations in plants. The active and inactive chromatin states are heritable and can be maintained or even be amplified by positive feedback in a transgenerational manner. Ho...
  3. A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly.

    Nature Genetics 47(4):405 (2015) PMID 25751626

    In Batesian mimicry, animals avoid predation by resembling distasteful models. In the swallowtail butterfly Papilio polytes, only mimetic-form females resemble the unpalatable butterfly Pachliopta aristolochiae. A recent report showed that a single gene, doublesex (dsx), controls this mimicry; h...
  4. A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries.

    PLoS ONE 10(2):e0116997 (2015) PMID 25646755 PMCID PMC4315571

    A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After...
  5. A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries.

    PLoS ONE 10(2):e0116997 (2015) PMID 25646755

    A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After...
  6. Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45 (NBRC 110737), Isolated from a Phenanthrene-Degrading Consortium.

    Genome Announcements 3(4) (2015) PMID 26184940 PMCID PMC4505128

    A phenanthrene degrader, Mycobacterium sp. EPa45, was isolated from a phenanthrene-degrading consortium. Here, we report the complete genome sequence of EPa45, which has a 6.2-Mb single circular chromosome. We propose a phenanthrene degradation pathway in EPa45 based on the complete genome seque...
  7. A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.

    PLoS ONE 10(2):e0116997 (2015) PMID 25646755 PMCID PMC4315571

    A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After...
  8. A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries.

    PLoS ONE 10(2):e0116997 (2015) PMID 25646755 PMCID PMC4315571

    A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After...
  9. Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation.

    BMC Genomics 16(1):80 (2015) PMID 25758444 PMCID PMC4334915

    Social amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species, the stalk is filled with motile stalk cells, as represented by the model organism Dic...
  10. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

    Genome Research 24(8):1384 (2014) PMID 24755901 PMCID PMC4120091

    Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing d...
  11. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

    Genome Research 24(8):1384 (2014) PMID 24755901 PMCID PMC4120091

    Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing d...
  12. A cDNA resource for gene expression studies of a hemichordate, Ptychodera flava.

    Zoological Science 31(7):414 (2014) PMID 25001912

    Recent investigations into the evolution of deuterostomes and the origin of chordates have paid considerable attention to hemichordates (acorn worms), as hemichordates and echinoderms are the closest chordate relatives. The present study prepared cDNA libraries from Ptychodera flava, to study ex...
  13. A cDNA resource for gene expression studies of a hemichordate, Ptychodera flava.

    Zoological Science 31(7):414 (2014) PMID 25001912

    Recent investigations into the evolution of deuterostomes and the origin of chordates have paid considerable attention to hemichordates (acorn worms), as hemichordates and echinoderms are the closest chordate relatives. The present study prepared cDNA libraries from Ptychodera flava, to study ex...
  14. Histone H4 Lys 20 Monomethylation of the CENP-A Nucleosome Is Essential for Kinetochore Assembly

    Developmental Cell 29(6):740 (2014) PMID 24960696 PMCID PMC4081567

    In vertebrate cells, centromeres are specified epigenetically through the deposition of the centromere-specific histone CENP-A. Following CENP-A deposition, additional proteins are assembled on centromeric chromatin. However, it remains unknown whether additional epigenetic features of...
  15. Histone H4 Lys 20 monomethylation of the CENP-A nucleosome is essential for kinetochore assembly.

    Developmental Cell 29(6):740 (2014) PMID 24960696 PMCID PMC4081567

    In vertebrate cells, centromeres are specified epigenetically through the deposition of the centromere-specific histone CENP-A. Following CENP-A deposition, additional proteins are assembled on centromeric chromatin. However, it remains unknown whether additional epigenetic features of centromer...
  16. Histone H4 Lys 20 monomethylation of the CENP-A nucleosome is essential for kinetochore assembly.

    Developmental Cell 29(6):740 (2014) PMID 24960696 PMCID PMC4081567

    In vertebrate cells, centromeres are specified epigenetically through the deposition of the centromere-specific histone CENP-A. Following CENP-A deposition, additional proteins are assembled on centromeric chromatin. However, it remains unknown whether additional epigenetic features of centromer...
  17. Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2.

    Environmental Microbiology Reports 6(3):268 (2014) PMID 24983531

    Several thermophilic hydrogenotrophic methanogens naturally aggregate in their habitats in association with hydrogen-producing bacteria for efficient transfer of the methane fermentation intermediates to produce methane. However, physiology of aggregation and the identity of aggregation-specific...
  18. Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2.

    Environmental Microbiology Reports 6(3):268 (2014) PMID 24983531

    Several thermophilic hydrogenotrophic methanogens naturally aggregate in their habitats in association with hydrogen-producing bacteria for efficient transfer of the methane fermentation intermediates to produce methane. However, physiology of aggregation and the identity of aggregation-specific...
  19. Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2.

    Environmental Microbiology Reports 6(3):268 (2014) PMID 24983531

    Several thermophilic hydrogenotrophic methanogens naturally aggregate in their habitats in association with hydrogen-producing bacteria for efficient transfer of the methane fermentation intermediates to produce methane. However, physiology of aggregation and the identity of aggregation-specific...
  20. Sex-specific posttranslational regulation of the gamete fusogen GCS1 in the isogamous volvocine alga Gonium pectorale.

    Eukaryotic Cell 13(5):648 (2014) PMID 24632243 PMCID PMC4060472

    Male and female, generally defined based on differences in gamete size and motility, likely have multiple independent origins, appearing to have evolved from isogamous organisms in various eukaryotic lineages. Recent studies of the gamete fusogen GCS1/HAP2 indicate that this protein is deeply co...