Abstract
Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and chimaeras, and the lack of established whole-genome sequences for the former has prevented our understanding of early vertebrate evolution and the unique phenotypes of elasmobranchs. Here we present de novo whole-genome assemblies of brownbanded bamboo shark and cloudy catshark and an improved assembly of the whale shark genome. These relatively large genomes (3.8–6.7 Gbp) contain sparse distributions of coding genes and regulatory elements and exhibit reduced molecular evolutionary rates. Our thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches. We also show the early establishment of the genetic machinery governing mammalian homoeostasis and reproduction at the jawed vertebrate ancestor. This study, supported by genomic, transcriptomic and epigenomic resources, provides a foundation for the comprehensive, molecular exploration of phenotypes unique to sharks and insights into the evolutionary origins of vertebrates.
Highlights
Our analysis revealed some conserved noncoding elements (CNEs) retained by elasmobranchs but missing in teleost fish and C. milii, which included a CNE in an intron of the Tbx[4] gene (Fig. 2b) previously reported as the core lung mesenchyme-specific enhancer[9]
To further characterize phenotypic traits refined in jawed vertebrates, we focused on gene repertories encoding endocrine hormones and their receptors that control growth, reproduction and homoeostasis
Oviparous species that allow captive breeding for continuous animal experimentation including embryonic operation
Summary
We searched for elasmobranch homologues of human long noncoding RNAs (lncRNAs), which again revealed more candidate homologues than in teleost fishes (Supplementary Note 14) These were screened for transcript evidence in bamboo shark RNA-seq data and absence of homology to coding sequences. The inclusion of the putative bamboo shark Malat[1] homologue in our result validates our screening procedure and more importantly, ascertains its noncoding transcription in a chondrichthyan species Overall, these findings indicate that despite the variable genome sizes and repetitive element compositions, elasmobranch genomes have undergone less modification in noncoding regions involved in gene regulation since the jawed vertebrate ancestor than is inferred by their evolutionary distance.
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