Comparative genomics illuminates karyotype and sex chromosome evolution of sharks

Abstract

Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.

Keywords: cartilaginous fish; dosage compensation; microchromosome; sex chromosome; shark; vertebrate karyotype.

Graphical abstract

Figure 1

Phylogenetic and comparative analyses of 11 gnathostome genomes (A) The divergence time is labeled at each node with a 95% confidence interval. Black asterisks denote the fossil calibration nodes. (B) The haploid number is shown for each species. Asterisks denote estimated haploid numbers according to Hi-C scaffolding without cytogenetic evidence. (C and D) The WSB shark has the largest assembled genome sizes (C) and repeat content (D). (E) Synteny between chicken and WSB shark is conserved. Chromosome IDs marked in red represent microchromosomes shared by the two species, while blue and violet mark chicken- and WSB-shark-specific microchromosomes, respectively. (F) Gene-order synteny between chicken (chr10 and chr6), WSB shark, and amphioxus homologous chromosomes. WSB shark chr42 has mixing orthologs of two different amphioxus chromosomes, while chr43 is homologous with a single amphioxus chromosome. Blue, red, lilac, and green colors represent genes on chromosomes 1, 20, 2, and 16, respectively. (G) The proposed model of microchromosome changes across vertebrate phylogeny.

Figure 2

Chromosomal synteny across cartilaginous fishes Any homologous chromosome involving chromosomal changes in elephant fish is highlighted in colors. The homologs of shark X chromosomes are highlighted in red. The chromosome IDs of the elephant fish are renamed according to the size rank, with their original IDs shown in Table S5. The inferred ancestral chromosomal number is labeled at each node.

Figure 3

Complex evolutionary history of shark sex chromosomes (A) The Y chromosome has a female-to-male (f/m) coverage ratio close to zero, but this ratio is close to one for the X. The X also shows an almost 2-fold f/m depth ratio, consistent with the hemizygous status of the X. (B) The top shows the Hi-C interaction map for the Y chromosome. The bar charts on the bottom show male and female HiFi sequencing coverage and satellite DNA percentage. The gene ZBTB39 is located in a young evolutionary stratum but very close to the PAR. In the first identity image, colored vertical bars represent the sequence identity between the X and Y chromosomes. The second identity image shows the alignment of the Y chromosome segments with 23 autosomes, with blue, orange, and red lines representing sequencing identities of 85%–90%, 90%–95%, and 95%–100%, respectively. The light blue and light red backgrounds indicate the young evolutionary stratum and the PAR, respectively. (C) Almost absent of SNPs on the X and Y chromosomes in males while the X chromosome shows a comparable SNP density relative to autosomes (chr12 is shown as one example) in females. (D) Fluorescence in situ hybridization (FISH) verification for Y chromosome. Blue fluorescence represents DAPI, and red fluorescence represents the signal of a Y-linked satellite DNA. (E) The gene SHARKY1 shows zero coverage by female HiFi or RNA sequencing (RNA-seq) coverage but is covered by male HiFi (hemizygous) and RNA-seq reads. m, male; f, female. (F) The gametologous tree for ZBTB39 shows that the gametologs are clustered by species rather than by chromosomes, suggesting an independent origin of the non-recombining region in the WSB shark, epaulette shark, and great white shark.

Figure 4

Shark sex chromosomes evolved gene-by-gene dosage compensation (A) The X-linked genes have a lower m/f expression ratio relative to autosomal genes. (B) In male tissues, the X-linked genes have lower expression levels relative to autosome genes. (C) 26 genes (denoted by orange bars) exhibit balanced gene expression between males and females, termed DC genes. (D) DC genes are more dosage sensitive than non-DC genes. (E) The expression levels of DC genes are significantly higher than non-DC genes in both females and males. (F) DC genes tend to be more broadly expressed but without a significantly lower tau value. (G) Comparison between mammal, avian, sturgeon, and shark sex chromosome features. The bottom and top horizontal lines in the boxplot represent the quartiles, while the middle horizontal lines represent the median. ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001 (Wilcoxon rank-sum test).