A telomere-to-telomere gap-free genome assembly of the protandrous hermaphrodite Asian seabass (Lates calcarifer)

Abstract

As a protandrous hermaphroditic fish species with natural sex change from male to female, Asian seabass (Lates calcarifer) represents an attractive model for studying sequential hermaphroditism. In this study, we constructed the first telomere-to-telomere (T2T) gap-free genome assembly of Asian seabass, by integration of MGI short-read, PacBio HiFi long-read, ONT ultra-long and Hi-C sequencing technologies. The haplotypic 614.19 Mb genome sequences were successfully anchored onto 24 chromosomes, demonstrating exceptional contiguity with a contig N50 of 26.57 Mb. Comprehensive annotation revealed precise localization of telomeric repeats and centromeric regions across various chromosomes. Good results from Merqury (QV: 57.8), CRAQ (99.45%) and BUSCO (100%) indicate a high level of accuracy for the assembled genome. ONT ultra-long and PacBio HiFi sequencing data were aligned with the assembly using minimap2, resulting in a mapping rate over 98%. Repetitive elements accounted for 18.18% (111.64 Mb) of the entire genome, and a total of 25,093 protein-coding genes were annotated. This high-quality T2T genome assembly provides a valuable genetic resource for in-depth comparative genomics, population genetics, molecular breeding, and functional studies of this economically important marine species. This reference assembly also facilitates investigations into the detailed molecular mechanisms underlying its unique reproductive strategy of the protandrous hermaphrodite Asian seabass.

Fig. 1

Asian seabass and its whole-genome sequence distribution. (A) A morphological image of the sequenced Asian seabass. (B) A k-mer (21-mer) distribution curve for estimation of the genome size.

Fig. 2

The first T2T genome assembly of Asian seabass. (A) Genome-wide chromatin interactions at a 500-kb resolution. Color blocks represent corresponding interactions, with various strengths from yellow (low) to red (high). (B) A Circos plot of the main genome features. From outside to inside include the 24 chromosomes, gene density, GC content, repetitive sequences density, and a colinear relationship among chromosomes of the Asian seabass genome assembly. Note that the density calculation window is set as 100 kb.

Fig. 3

Genome-wide localization of repetitive elements (REs), telomeres and centromeres. The triangles at both ends of each chromosome represent the telomere regions, and the gully area within each chromosome stands for the centromere region.