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Nat Ecol Evol
2020 Jun 20;46:820-830. doi: 10.1038/s41559-020-1156-z.
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Deeply conserved synteny resolves early events in vertebrate evolution.
Simakov O
,
Marlétaz F
,
Yue JX
,
O'Connell B
,
Jenkins J
,
Brandt A
,
Calef R
,
Tung CH
,
Huang TK
,
Schmutz J
,
Satoh N
,
Yu JK
,
Putnam NH
,
Green RE
,
Rokhsar DS
.
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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.
Extended Data Fig. 1. Chromatin and genetic maps of amphioxus genome. (a): Chromatin conformation capture contact map for amphioxus genome assembly. Density of read-pairs representing three-dimensional chromatin contacts are shown as a heat map. (b): Maternal meiotic linkage map of amphioxus from a 96 progeny F1 cross. Markers represent phased 500 kb windows of the chromosomal assembly; consecutive windows are combined when there is no evidence for recombination in the genotyped progeny. Amphioxus linkage groups and the 19 longest assembled scaffolds are in 1:1 correspondence, confirming the Hi-C-based chromosome-scale assembly. (See Supplementary Note 4.).
Fig. 1. Conserved syntenies between amphioxus and various species. a, Oxford dot plot of orthologous genes between amphioxus and two representative bony vertebrates: spotted gar (Lepisosteus oculatus; top) and chicken (Gallus gallus; bottom). The axes show the index of 6,843 orthologous gene families anchored by mutual best hits from gar, chick, frog and human to amphioxus, with chromosome boundaries indicated. Dashed vertical lines show the location of synteny breakpoints for amphioxus that are consistent in comparisons with other vertebrate (Extended Data Figs. 2 and 3) and invertebrate genomes (see b; Extended Data Fig. 4). Genes are coloured according to this partitioning, defining 17 ancestral CLGs, with labels shown to the right. b, Mutual best-hit dot plot of amphioxus versus scallop, using the same colouring as in a. Syntenic discontinuities in amphioxus (indicated by the dashed lines) are consistent in the scallop. Note that CLGB (dark purple) is distributed across three pairs of homologous chromosomes, implying that this CLG existed as three distinct linkage groups in the scallop–amphioxus common ancestor.
