Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

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  • Jun Inoue
    Mathematical Biology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan;
  • Yukuto Sato
    Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan;
  • Robert Sinclair
    Mathematical Biology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan;
  • Katsumi Tsukamoto
    Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan;
  • Mutsumi Nishida
    Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan;

抄録

<jats:title>Significance</jats:title> <jats:p>All genes are duplicated by whole-genome duplication (WGD), reverting in number over time, but the actual timing of genome reshaping through gene loss remains poorly understood. We estimated the spatiotemporal loss/persistence pattern of 6,892 gene lineage pairs after the teleost-specific WGD, using careful orthology assignment and a reliable time-calibrated tree. We found that massive gene loss did occur in the first 60 My, mainly due to events involving the simultaneous loss of multiple redundant genes, and the rate of loss then slowed to an approximately constant level for the subsequent 250 My. Similar genomic gene arrangements within teleosts imply that rapid gene loss led to the reshaping of the teleost genomes before their major divergence.</jats:p>

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