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. 2024 Jan 29;14(3):434.
doi: 10.3390/ani14030434.

Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus

Fang-Yuan Han  1 , Ren-Xie Wu  1 , Ben-Ben Miao  2 , Su-Fang Niu  1 , Qing-Hua Wang  3 , Zhen-Bang Liang  1
Affiliations

Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus

Fang-Yuan Han et al. Animals (Basel). .

Abstract

Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids.

Keywords: Eupleurogrammus muticus; comparative genomics; genome sequencing; positive selection.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
E. muticus used for sequencing.
Figure 2
Figure 2
Chromosome interaction mapping (A) and genome-wide interaction mapping (B). The color reflects the intensity of each contact, with deeper colors representing higher intensity.
Figure 3
Figure 3
Circle figure of the genomic characteristics of E. muticus, including (a) the GC content of the genome, (b) the distribution of genes, (c) the distribution of repeats, (d) the distribution of long tandem repeats, (e) the distribution of long interspersed nuclear elements, and (f) the distribution of DNA transposable elements.
Figure 4
Figure 4
The numbers of homologous genes in 20 fish species (A) and Venn diagram of the homologous gene families between E. muticus and three closely related species (B).
Figure 5
Figure 5
The expanded and contracted gene families of the 20 fish species during in the evolutionary process.
Figure 6
Figure 6
Divergence time estimates of the 20 fish species.
Figure 7
Figure 7
Collinearity analysis of E. muticus and L. savala based on coding sequences.
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