Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

•De novo reference genome assemblies of four non-teleost ray-finned fishes•Basal fishes have key limb development regulatory elements•Lung-related genes in early hold the for lung origin•Cardio-respiratory systems’ co-evolution during air breathing evolution Rich fossil evidence suggests that many traits and functions related to terrestrial were present long before ancestor lobe- fishes. Here, we sequences bichir, paddlefish, bowfin, alligator gar, covering all major divergent lineages Our analyses show these species exhibit mosaic genomic features In particular, elements are fishes, supporting hypothesis relevant ancestral regulation networks emerged origin tetrapods. Transcriptome confirm homology between swim bladder reveal presence functional lung-related Furthermore, functionally validate essential role a jawed vertebrate highly conserved element cardiovascular development. results imply ancestors vertebrates already had potential gene cardio-respiratory systems breathing. 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Remarkably, higher synteny chicken than whose undergone more fusions, fissions, rearrangements following teleost-specific 2B S2B). example, found 51% genome. When expanding include vertebrates, share 9%–36% humans, shared any teleosts (6%–7%) examined humans S2). clearly indicate largely preserved structure duplication. overall conservation genome, 22 fusion appear lineage, micro-chromosomes merged macro-chromosomes. rearrangement accompanied elevated activity, increases species.Figure S2The WGD 2Show caption(A) reconstruction procedure.(B) bichir-spotted gar-chicken gar-zebrafish-medaka.(C) HOX clusters vertebrates.(D) 4DTv determine 3R time sterlet.(E) Construction 1935 among (g), (p) (s). green represents independent sterlet. orange WGD. purple cannot prove whether independently not. pie chart proportion topologies.View Large Image ViewerDownload Hi-res image Download (PPT) (A) procedure. (B) gar-zebrafish-medaka. (C) (D) (E) topologies. Recent shown third round (3R WGD) (Acipenser ruthenus) (Du closely paddlefish. detected seven Hox indicating S2C). To investigate event lineages, analyzed distributions synonymous substitution rates (Ks) 4-fold degenerative third-codon transversions (4dTv) 3,743 8,297 paralogs. Ks age different ranges, suggesting 2C). pattern distribution 4dTv values, S2D S2E). Based (135 1), 121 Mya 51 Mya, respectively. Although our estimated much study, prior sterlet-Atlantic 166 earlier (74 (Rabosky 2013Rabosky D.L. Santini F. Eastman S.A. Sidlauskas Chang Alfaro M.E. 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