Deeply conserved synteny resolves early events in vertebrate evolution

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

doi:10.1038/s41559-020-1156-z

Deeply conserved synteny resolves early events in vertebrate evolution

Journal Article · Mon Apr 20 00:00:00 EDT 2020 · Nature Ecology and Evolution

DOI:https://doi.org/10.1038/s41559-020-1156-z· OSTI ID:1817164

^[1]; ^[2]; ^[3]; ^[4]; ^[5]; Brandt, Alexander ^[6]; Calef, Robert ^[7]; Tung, Che-Huang ^[8]; Huang, Tzu-Kai ^[9]; ^[5]; ^[10]; ^[9]; ^[7]; Green, Richard E. ^[11]; ^[12]

Okinawa Inst. of Science and Technology Graduate Univ., Okinawa (Japan). Molecular Genetics Unit; Univ. of Vienna (Austria). Dept. of Neuroscience and Developmental Biology; OSTI
Okinawa Inst. of Science and Technology Graduate Univ., Okinawa (Japan). Molecular Genetics Unit
Université Côte d’Azur, Nice (France). Centre National de la Recherche Scientifique (CNRS). INSERM. IRCAN
Univ. of California, Santa Cruz, CA (United States). Dept. of Biomolecular Engineering
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Univ. of California, Berkeley, CA (United States). Dept. of Molecular and Cell Biology
Dovetail Genomics, Scotts Valley, CA (United States)
Academia Sinica, Taipei (Taiwan). Inst. of Cellular and Organismic Biology
Academia Sinica, Taipei (Taiwan). Inst. of Cellular and Organismic Biology
Okinawa Inst. of Science and Technology Graduate Univ., Okinawa (Japan). Marine Genomics Unit
Univ. of California, Santa Cruz, CA (United States). Dept. of Biomolecular Engineering
Okinawa Inst. of Science and Technology Graduate Univ., Okinawa (Japan). Molecular Genetics Unit; Univ. of California, Berkeley, CA (United States). Dept. of Molecular and Cell Biology; Chan Zuckerberg Biohub, San Francisco, CA (United States)

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. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid–late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1817164

Journal Information:: Nature Ecology and Evolution, Journal Name: Nature Ecology and Evolution Journal Issue: 6 Vol. 4; ISSN 2397-334X

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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