The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish

Abstract

Chondrichthyan (cartilaginous fish) occupies a key phylogenetic position and is important for investigating evolutionary processes of vertebrates. However, limited whole genomes impede our in-depth knowledge of important issues such as chromosome evolution and immunity. Here, we report the chromosome-level genome of white-spotted bamboo shark. Combing it with other shark genomes, we reconstructed 16 ancestral chromosomes of bamboo shark and illustrate a dynamic chromosome rearrangement process. We found that genes on 13 fast-evolving chromosomes can be enriched in immune-related pathways. And two chromosomes contain important genes that can be used to develop single-chain antibodies, which were shown to have high affinity to human disease markers by using enzyme-linked immunosorbent assay. We also found three bone formation-related genes were lost due to chromosome rearrangements. Our study highlights the importance of chromosome rearrangements, providing resources for understanding of cartilaginous fish diversification and potential application of single-chain antibodies.

The whale shark genome reveals patterns of vertebrate gene family evolution

“…Alongside the work on the whale shark genome, genomes have also been assembled for the bamboo shark ( Chiloscyllium punctatum ), cloudy catshark ( Scyliorhinhus torazame ), white shark ( Carharodon carcharias ), and white-spotted bamboo shark ( Chiloscyllium plagiosum ). Comparative analyses of shark genomes supported numerous evolutionary implications of shark genome evolution, including a slow rate of shark genome evolution, a reduction in olfactory gene diversity, positive selection of wound healing genes, proliferation of CR1-like LINEs within introns related to their larger genomes, and rapid evolution in immune-related genes ( Hara et al, 2018 ; Marra et al, 2019 ; Weber et al, 2020 ; Zhang et al, 2020 ).…”

Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

“…The P2RX3 and P2RX2 genes are subunits of the P2X gene family. P2X receptors are non-selective cation channels gated by extracellular ATP and exhibit relatively high Ca 2+ permeability [ 87 ]; the P2rx2 receptor mainly functions in sensory neurons, neuromuscular junction formation, whereas P2RX3 , with multiple copies, were found in bony fishes [ 88 ].…”

State of Shark and Ray Genomics in an Era of Extinction

“…Other published chondrichthyan genomes are from the Elasmobranchii subclass and are currently limited to two skates: little skate (Leucoraja erinacea) (Wyffels et al, 2014) and thorny skate (Amblyraja radiata) (Rhie and Project, 2021), and (Venkatesh et al, 2014;NCBI, 2021a), Hydrolagus affinis (Fonseca et al, 2020), Scyliorhinus torazame (Hara et al, 2018), Scyliorhinus canicular (NCBI, 2021c), Carcharodon carcharias (Marra et al, 2019;NCBI, 2021b), Rhincodon typus (Read et al, 2017;Weber et al, 2020), Chiloscyllium punctatum (Hara et al, 2018;Hoencamp et al, 2021), Chiloscyllium plagiosum (Zhang et al, 2020), Pristis pectinata (NCBI, 2019b), Amblyraja radiata (Rhie et al, 2020), and Leucoraja erinacea (Wyffels et al, 2014). Scale at bottom displays where different classifications diverged.…”

“…five sharks: whale shark (Rhincodon typus) (Read et al, 2017;Weber et al, 2020), brownbanded bamboo shark (Chiloscyllium punctatum) (Hara et al, 2018;Hoencamp et al, 2021), cloudy catshark (Scyliorhinus torazame) (Hara et al, 2018), great white shark (Carcharodon carcharias) (Marra et al, 2019), and whitespotted bamboo shark (Chiloscyllium plagiosum) (Zhang et al, 2020; Figure 1). Draft genomes for other elasmobranch species are publicly available online but have not yet been formally published, including the smalltooth sawfish (Pristis pectinata) (NCBI, 2019b), small-spotted catshark (Scyliorhinus canicula) (NCBI, 2021c), and chromosome-length white shark assembly (NCBI, 2021b; Figure 1).…”

“…In these following recent investigations, chromosomelength chondrichthyan genome assemblies have allowed the reconstruction of ancestral vertebrate chromosomes, chromosomal rearrangements, and breakages as well as the evolution of immune responses that show potential for human disease treatments (Zhang et al, 2020). Additionally, investigation of the small-eyed rabbitfish genome showed the evolution of the endocrine systems in early jawed vertebrates through a comparative analysis of nuclear receptors (NRs) in these chondrichthyan genomes (Fonseca et al, 2020).…”