Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

Abstract

Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.

Keywords: Pseudobagrus ussuriensis; chromosome evolution; sex chromosome; sex-determining region; whole-genome sequencing.

Figure 1.

Genome assembly of Pseudobagrus ussuriensis. (A) The chromosomal-crosstalk heatmap based on Hi-C data. The blocks represent the contacts between one location and another. The color reflects the intensity of each contact, with deeper colors representing higher intensity. (B) Genome characteristics of P. ussuriensis, from outer to inner circles: a, the 26 chromosomes at the Mb scale; b–e, GC content, SNP density, repeat density and gene density across the genome, respectively, drawn in 1 Mb nonoverlapping windows.

Figure 2.

Phylogenomic trees between Pseudobagrus ussuriensis and other fishes. (A) Phylogenetic tree between P. ussuriensis and another 11 fishes. (B) Divergence time tree between P. ussuriensis and another 11 fish species. Numbers on the branches represent estimated diverge times in millions of years ago, and nodes marked with red circles indicate the calibration time from fossil. (C) Expansion and contraction of gene families in P. ussuriensis. MRCA stands for the most recent common ancestor; pie charts and numbers represent the proportion and numbers of gene families with expansion marked with green and contraction marked with red, respectively.

Figure 3.

Chromosomal syntenic relationships and estimated chromosome evolution processes between Pseudobagrus ussuriensis and another four catfishes. (A) The syntenic relationships among chromosomes of P. ussuriensis (P. uss), Pelteobagrus fulvidraco (P. ful), and Ictalurus punctatus (I. pun). (B) The syntenic relationships among chromosomes of P. ussuriensis (P. uss), Silurus meridionalis (S. mer), and Pangasianodon hypophthalmus (P. hyp). (C)–(F) Estimated catfish chromosome evolution clusters 1–4, Pu P. ussuriensis, Pf P. fulvidraco, Ip I. punctatus, Sm S. meridionalis, and Ph P. hypophthalmus. (G) The estimated evolution process of 26 chromosomes in Pseudobagrus ussuriensis.