While this represented an important step forward for elasmobranch genomics, the assemblies were fragmentary, and substantial improvements to the genome contiguity and annotation were expected from reassembling the genome using PacBio long-read sequences ( Read et al., 2017).ĭespite the relative lack of genomic information prior, much recent work has focused upon further sequencing, assembling, and analyzing of the whale shark nuclear genome ( Hara et al., 2018 Read et al., 2017 Weber et al., 2020). A toll-like receptor (TLR) similar to TLR21 was also found in this first whale shark genome draft assembly, suggesting that TLR21 was derived in the most recent common ancestor (MRCA) of jawed vertebrates. Due to its phylogenetic position relative to other vertebrates, the scarcity of shark genomes, and its unique biology, the previous whale shark genome assemblies were used to address questions related to vertebrate genome evolution ( Hara et al., 2018 Marra et al., 2019), the relationship of gene evolution in sharks and unique shark traits ( Hara et al., 2018 Marra et al., 2019), as well as the evolution of gigantism ( Weber et al., 2020). Famously representing one of Earth’s ocean giants, the whale shark is by far the largest of all extant fishes, reaching a maximum confirmed length of nearly 19 m ( McClain et al., 2015). The first draft elasmobranch genome published was for a male whale shark of Taiwanese origin by Read et al., 2017. Until recently, few genetic resources have been available for elasmobranchs in general, and for the whale shark ( Rhincodon typus) in particular. Sampling other elasmobranch genomes for comparison is therefore critically important to our understanding of vertebrate genome evolution ( Redmond et al., 2018). milii separated from the Elasmobranchii (sharks, rays, and skates) ~420 million years ago, shortly after the divergence from bony vertebrates. As a member of the Holocephali (chimaeras, ratfishes), one of the two major groups of cartilaginous fishes, C. ![]() The first cartilaginous fish genome, that of Callorhinchus milii (known colloquially as ghost shark, elephant shark, or elephant fish), was used to study the early evolution of genes related to bone development and emergence of the adaptive immune system ( Venkatesh et al., 2014). Until very recently, genomic data from cartilaginous fishes were significantly underrepresented compared to other vertebrate lineages. The availability of sequence data from many species across vertebrate lineages is key to the success of such studies. Comparison of genomes between these two groups not only provides insight into early gnathostome evolution and the emergence of various biological features, but also enables inference of ancestral jawed vertebrate traits ( Venkatesh et al., 2014). Jawed vertebrates (Gnathostomata) comprise two extant major groups, the cartilaginous fishes (Chondrichthyes) and the bony vertebrates (Osteichthyes, including Tetrapoda) ( Venkatesh et al., 2014). Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. We also discovered a new toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. ![]() We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied.
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