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Fig. S9
Identification of a gene lost in tetrapods, the Atonal homolog 1b (Atoh1b) gene. A) In EnsemblCompara GeneTree ENSGT00630000089619, two Atoh1 gene clades are apparent: Atoh1a, present in teleosts, Latimeria, and tetrapods, and Atoh1b, present in teleosts and Latimeria only. B) and C) Dotplots of zebrafish (Dre) vs. human (Hsa) chromosomes from the Synteny Database. B)
The zebrafish atoh1b gene region on Dre14 shares conserved syntenies with human chromsomes Hsa4 (containing ATOH1A) and Hsa5 (no ATOH1 gene present). Zebrafish atoh1b is found on Dre8 (not shown). Human chromosomes Hsa4 and Hsa5 are derived from the ancestral vertebrate chromosome C. C) Orthologs of the genes flanking atoh1b, tspan17 and dok3, are found on Hsa5, which shows double conserved synteny with Dre14 (containing atoh1b) and Dre21, as result of the teleost genome duplication.
The combination of phylogenetic (A) and syntenic (B, C) data provides evidence that an Atoh1 gene on the ancestral vertebrate chromosome C was duplicated in the course of the two rounds of vertebrate genome duplication. The Atoh1a paralog (ohnolog) was retained in all bony vertebrate lineages (ray-finned and lobe-finned fish, including tetrapods), while Atoh1b was lost in tetrapods from a region located on Hsa5 in the human genome.