Whole-Genome Sequencing Analyses Reveal the Evolution Mechanisms of Typical Biological Features of Decapterus maruadsi

TL;DR

This study provides a high-quality genome for Decapterus maruadsi, revealing genes linked to its fast growth, small size, and high reproduction.

Contribution

The paper presents a chromosome-level genome assembly and identifies genes under positive selection related to key biological traits in D. maruadsi.

Findings

A high-quality genome of D. maruadsi was assembled with 23 chromosomes and 22,716 annotated protein-coding genes.

Genes related to bone, muscle, cardioid, and ovary development were found under positive selection, explaining its biological traits.

The genome resource supports future research in genetic conservation and adaptive evolution of D. maruadsi.

Abstract

In this study, a high-quality chromosomal-level genome of male Decapterus maruadsi was assembled based on Illumina, PacBio, and Hi-C technology. Notably, 23 chromosome-level genome sequences with lengths ranging between 21.74 and 44.53 Mb were assembled. A total of 22,716 protein-coding genes with an average transcript and a CDs length of 12,823.03 bp and 1676.66 bp, respectively, were successfully annotated. Based on positive selection analysis, some genes associated with the growth and development of bone, muscle, cardioid, and ovary were screened. These genes were likely involved in the evolution of typical biological features in D. maruadsi, such as fast growth rate, small body size, and strong fecundity. The newly established reference genome provides a fundamental genome resource for further genetic conservation, genomic-assisted breeding, and exploration of the molecular mechanism underlying adaptive evolution.

Decapterus maruadsi is a typical representative of small pelagic fish characterized by fast growth rate, small body size, and high fecundity. It is a high-quality marine commercial fish with high nutritional value. However, the underlying genetics and genomics research focused on D. maruadsi is not comprehensive. Herein, a high-quality chromosome-level genome of a male D. maruadsi was assembled. The assembled genome length was 716.13 Mb with contig N50 of 19.70 Mb. Notably, we successfully anchored 95.73% contig sequences into 23 chromosomes with a total length of 685.54 Mb and a scaffold N50 of 30.77 Mb. A total of 22,716 protein-coding genes, 274.90 Mb repeat sequences, and 10,060 ncRNAs were predicted, among which 22,037 (97%) genes were successfully functionally annotated. The comparative genome analysis identified 459 unique, 73 expanded, and 52 contracted gene families. Moreover, 2804 genes were identified as candidates for positive selection, of which some that were related to the growth and development of bone, muscle, cardioid, and ovaries, such as some members of the TGF-β superfamily, were likely involved in the evolution of typical biological features in D. maruadsi. The study provides an accurate and complete chromosome-level reference genome for further genetic conservation, genomic-assisted breeding, and adaptive evolution research for D. maruadsi.

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