Search Results 1-20 of 985

  • Thermotogales origin scenario of eukaryogenesis

    桑原 朋彦 , Tomohiko KUWABARA , Kensuke Igarashi

    … We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). … Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. …

    Journal of Theoretical Biology (492), 110192, 2020-05

    IR 

  • Deeply conserved synteny resolves early events in vertebrate evolution

    Oleg Simakov , Ferdinand Marlétaz , Jia-Xing Yue , Brendan O'Connell , Jerry Jenkins , Alexander Brandt , Robert Calef , Che-Huang Tung , Tzu-Kai Huang , Jeremy Schmutz , Nori Satoh , Jr-Kai Yu , Nicholas H. Putnam , Richard E. Green , Daniel S. Rokhsar

    … Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. … All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). …

    Nature Ecology & Evolution, 2020-04-20

    IR 

  • Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome

    Nino A. Espinas , Le Ngoc Tu , Leonardo Furci , Yasuka Shimajiri , Yoshiko Harukawa , Saori Miura , Shohei Takuno , Hidetoshi Saze

    … Although TE-bearing introns are widely observed in eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, remain poorly understood. … In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. …

    PLOS Genetics 16(3), e1008637, 2020-03-18

    IR 

  • Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome

    Cai Li , Nicholas M. Luscombe

    … Nucleosome organization has been suggested to affect local mutation rates in the genome. … Depletion of strong nucleosomes in older transposons suggests frequent positioning changes during evolution. … The findings have important implications for human genetics and genome evolution. …

    Nature Communications 11(1), 1363, 2020-03-13

    IR 

  • Retrotransposons Manipulating Mammalian Skeletal Development in Chondrocytes

    Kubota Satoshi , Ishikawa Takanori , Kawata Kazumi , Hattori Takako , Nishida Takashi

    … Retrotransposons are genetic elements that copy and paste themselves in the host genome through transcription, reverse-transcription, and integration processes. … Along with their proliferation in the genome, retrotransposons inevitably modify host genes around the integration sites, and occasionally create novel genes. … As such, their profound role in the evolution of mammalian genomes is obvious; …

    International Journal of Molecular Sciences 21(5), 1564, 2020-02-25

    IR 

  • The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants

    Akagi Takashi , Shirasawa Kenta , Nagasaki Hideki , Hirakawa Hideki , Tao Ryutaro , Comai Luca , Henry Isabelle M.

    … Here, we developed a full draft of the diploid persimmon genome (D. … lotus), which revealed a lineage-specific whole-genome duplication event and provided information on the architecture of the Y chromosome. … Evolutionary analysis suggested that MeGI underwent adaptive evolution after the whole-genome duplication event. … We drafted the whole genome sequence of diploid persimmon to investigate their evolutionary history. …

    PLoS Genetics 16(2), e1008566, 2020-02-18

    IR 

  • The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants

    Akagi Takashi , Shirasawa Kenta , Nagasaki Hideki , Hirakawa Hideki , Tao Ryutaro , Comai Luca , Henry Isabelle M.

    … Here, we developed a full draft of the diploid persimmon genome (D. … lotus), which revealed a lineage-specific whole-genome duplication event and provided information on the architecture of the Y chromosome. … Evolutionary analysis suggested that MeGI underwent adaptive evolution after the whole-genome duplication event. …

    PLOS Genetics 16(2), 2020-02-18

    IR 

  • Primary orthologs from local sequence context

    Kun Gao , Jonathan Miller

    … Thus, sequence-, as opposed to gene-, centric modes of inferring paths of sequence evolution are increasingly relevant. … Context-dependent identification of orthologs traditionally relies on genomic context over length scales characteristic of conserved gene order or whole-genome sequence alignment, and can be computationally intensive. …

    BMC Bioinformatics 21(1), 48, 2020-02-06

    IR 

  • Sexuality in plants, unveiled from genome evolution  [in Japanese]

    赤木 剛士

    … Notwithstanding, in plants, evolution of sexual systems and mechanisms underlying these transitions have been little unveiled. … In persimmon, a recent genome triplication (hexaploidization) in cultivated persimmon (D. … On the other hand, an ancient Diospyros-specific paleo-genome duplication (paleo-tetraploidization) enabled neofunctionalization in the proto-MeGI, via positive selection, to establish a new function as a sex determinant. …

    岡山大学農学部学術報告 (109), 37-40, 2020-02-01

    IR 

  • Conceptual Operations based on Group Theory Logic : An Evolution from Word Sign to Concept (Digital Linguistics)  [in Japanese]

    得丸 久文

    電子情報通信学会技術研究報告 = IEICE technical report : 信学技報 119(394), 1-6, 2020-01-25

  • Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs

    Takeshi Takeuchi , Tetsuji Masaoka , Hideo Aoki , Ryo Koyanagi , Manabu Fujie , Noriyuki Satoh

    … We determined the population structure of the pearl oyster, Pinctada fucata, in the Indo-Pacific Ocean using genome-wide genotyping data from multiple sampling localities. … A genome scan showed evidence of adaptive evolution in genomic loci, possibly associated with changes in environmental factors, including SST and oxygen concentration. …

    Evolutionary Applications 13(4), 837-853, 2020-01-08

    IR 

  • Unravelling spiral cleavage

    José M. Martín-Durán , Ferdinand Marlétaz

    … This is one of the most widespread developmental programs in animals, probably ancestral to almost half of the animal phyla, and therefore its study is essential for understanding animal development and evolution. … Recent technical and conceptual advances, such as the establishment of genome editing and improved phylogenetic resolution, are paving the way for a fresher and deeper look into this fascinating early cleavage mode. …

    Development 147(1), dev181081, 2020-01-02

    IR 

  • International Workshop—Leveraging evolution into molecular breeding  [in Japanese]

    Sakuma Shun , Komatsuda Takao

    Breeding Research, 2020

    J-STAGE 

  • Genetic Information about Phenotype: A Teleosemantic Point of View  [in Japanese]

    ISHIDA Tomoko

    … <p>The common idea that a gene encodes a phenotypic character has played an important role in the theory of evolution, one of whose origin is population genetics. … It shows that phenotypic information is not carried by a single gene, but by a genome containing multiple genes and the regulatory regions which form the related gene networks.</p> …

    Journal of the Japan Association for Philosophy of Science 47(2), 59-79, 2020

    J-STAGE 

  • Molecular Pathogenesis and Treatment of Myelodysplastic Syndromes

    Nakajima Hideaki

    … Sequential acquisition of mutations in these sets of genes serves as a driver for the initiation, clonal evolution and progression of MDS. …

    Internal Medicine, 2020

    J-STAGE 

  • A Bird's-eye View of Glycan Diversity  [in Japanese]

    Suzuki Noriko

    … We cloned cDNAs of an α1,4-galactosyltransferase, which produce this carbohydrate antigens, from a pigeon liver cDNA library, and inferred how this glycans were acquired or lost during vertebrate evolution ranging from fish to birds and mammals, based on cDNA sequences and DNA databases. … Since the Human Genome Project, the availability of whole genome sequence data has grown enormously, and the number and scope of target species has expanded. …

    Trends in Glycoscience and Glycotechnology 32(185), J7-J12, 2020

    J-STAGE 

  • A Bird's-eye View of Glycan Diversity

    Suzuki Noriko

    … We cloned cDNAs of an α1,4-galactosyltransferase, which produce this carbohydrate antigens, from a pigeon liver cDNA library, and inferred how this glycans were acquired or lost during vertebrate evolution ranging from fish to birds and mammals, based on cDNA sequences and DNA databases. … Since the Human Genome Project, the availability of whole genome sequence data has grown enormously, and the number and scope of target species has expanded. …

    Trends in Glycoscience and Glycotechnology 32(185), E7-E12, 2020

    J-STAGE 

  • Evolution and phylogenetic position of Ulvophyceae inferred from molecular data  [in Japanese]

    市原 健介

    海洋と生物 41(6), 491-498, 2019-12

  • Human genome diversity of populations in East Asia  [in Japanese]

    徳永 勝士 , 河合 洋介

    腎臓内科・泌尿器科 = Nephrology & urology 10(6), 561-565, 2019-12

    Ichushi Web 

  • Antigenic Drift of Influenza A Virus〜Low-Dimensional Antigenic Evolution and Persistent Circulation〜  [in Japanese]

    渡部 輝明

    … During the antigenic drift,the substitutions occurred on the genome are subject to selection. … This approach enables us to understand two contrasting epidemiological characteristics of the influenza H3N2 subtype: the persistent circulation in the human population and the slim phylogenic tree for their antigenic evolution. … Here we review epidemiological characteristics of the antigenic evolution of influenza H3N2 subtype. …

    東北医科薬科大学研究誌 = Journal of Tohoku Medical and Pharmaceutical University (66), 1-9, 2019-12

    IR 

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