Genome and gene evolution of seahorse species revealed by the chromosome-level genome of Hippocampus abdominalis

Abstract

Seahorses belong to the teleost family Syngnathidae that evolved a distinct body plan and unique male pregnancy compared to other teleosts. As a classic model for studying evolution of viviparity and sexual selection of teleosts, seahorse species still lack a publicly available high-quality reference genome. Here, we generated the genome assembly of the big-belly seahorse, Hippocampus abdominalis with long-read and Hi-C technologies. We managed to place over 99% of the total length of 444.7 Mb of assembled genome into 21 linkage groups with almost no gaps. We reconstructed a phylogenomic tree with the big-belly seahorse genome and other representative Syngnathidae and teleost species. We also reconstructed the historical population dynamics of four representative Syngnathidae species. We found the gene families that underwent expansion or contraction in the Syngnathidae ancestor were enriched for immune-related or ion transporter gene ontology terms. Many of these genes were also reported to show a dynamic expression pattern during the pregnancy stages of H. abdominalis. We also identified putative positively selected genes in the Syngnathidae ancestor or in H. abdominalis, whose mouse mutants are enriched for abnormal craniofacial and limb morphological phenotypes. Overall, our study provides an important genome resource for evolutionary and developmental studies of seahorse species, and candidate genes for future experimental works.

Keywords: Hi-C; Seahorse; chromosome-level genome; male brood pouch.

FIGURE 1

Genomic features of the big‐belly seahorse, Hippocampus abdominalis. (a) The chromosome‐level genome assembly of the big‐belly seahorse was generated by combining PacBio long reads and Hi‐C reads. The Hi‐C contact map here shows the genome‐wide all‐by‐all interactions of 21 chromosomes, with little off‐diagonal interactions between chromosomes in this curated assembly. (b) Comparison of the scaffold length distributions between the big‐belly seahorse versus the other three Syngnathidae species produced by Illumina reads. (c) The histogram shows the distributions of sequence divergence between each repeat family versus their consensus sequences. (d) Compositional overview of chromosome 1 and its GC levels. The colour‐coded map shows 100 kb nonoverlapping sliding window plots. The colour code spans the spectrum of distinct GC levels, indicated by broken horizontal lines, from blue (GC‐poorest isochores) to red (GC‐richest isochores) (e) Gene density (gene number per Megabase) of GC isochores

FIGURE 2

Phylogeny and demographic history of the representative Syngnathidae species. (a–c) Collinearity analysis between H. abdominalis vs. H. comes, H. erectus and S. scovelli. We performed the collinearity analysis between H. abdominalis linkage groups and the scaffolds longer than 1 Mb in H. comes and H. erectus and linkage groups in S. scovelli. Blue segments represent alignments to the positive strand of H. abdominalis. Red segments represent alignments to the negative strand of H. abdominalis. Numbers in the parentheses are the number of scaffolds longer than 1Mb in H. comes and H. erectus, and the number of linkage groups in S. scovelli. (d) Maximum likelihood tree reconstructed using single‐copy orthologous genes. Branch lengths are scaled to the specific substitution rates estimated by PhyML. The numbers on each branch indicate the estimated divergence time (in million years), and 95% highest posterior densities. All phylogenetic nodes have full bootstrap support. (e) PSMC‐inferred trajectories of four syngnathid species. Coloured bold line of each species is the population size dynamics inferred from PSMC analyses, with the lighter, thinner lines indicating variations in population size derived from 100 bootstraps. Top rectangles show respective time periods with global temperature changes. LGP: last glacial period

FIGURE 3

Evolution of gene families of the big‐belly seahorse. (a) Venn diagram showing the specific and shared gene families of the four Syngnathidae species. (b) The inferred numbers of expanded (green) or contracted (red) gene families at each phylogenetic node of Syngnathidae species. We labelled the divergence time on each node. MRCA: most recent common ancestor. Animal icons are made by Freepik from www.flaticon.com, from https://thenounproject.com and from http://phylopic.org. (c) Enriched GO terms of expanded and contracted gene families identified by Metascape (Zhou et al., 2019). Nodes are coloured by their identities. Each node represents one enriched term. Within each branch, the size of nodes represents the percentage of input genes belonging to each GO term. Terms with Kappa scores (Cohen, 1960) >0.3 are connected by edges, the thicker, the higher similarity

FIGURE 4

Rapidly evolving genes of seahorse species. Phylogenetic distribution of enriched mutant phenotypes (MP) of mouse orthologues of seahorse genes. Each MP term is shown by an organ icon, and significantly enriched for genes undergoing positive selection (PSG, red) or relaxed selective constraints (RSG, grey) inferred by lineage‐specific PAML analyses. Organ icons are made from https://thenounproject.com. Gene examples that have undergone putative positive selection or relaxed selective constraints were labelled onto each branch