Whole-Genome Sequencing of <i>Hexagrammos otakii</i> Provides Insights into Its Genomic Characteristics and Population Dynamics
<i>Hexagrammos otakii</i>, also commonly called “Fat Greenling”, is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-03-01
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| Series: | Animals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2615/15/6/782 |
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| Summary: | <i>Hexagrammos otakii</i>, also commonly called “Fat Greenling”, is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of <i>H. otakii</i>, generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the <i>H. otakii</i> genome, followed by microsatellites. In the phylogenetic tree, <i>H. otakii</i> was placed within a well-supported clade (bootstrap support = 100%) that included <i>S. sinica</i>, <i>N. coibor</i>, <i>L. crocea</i>, and <i>C. lucidus</i>. PSMC analysis revealed that <i>H. otakii</i> underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (~70–15 Kya), with no significant recovery observed by ~10 Kya. This study was a comprehensive genome survey analysis of <i>H. otakii</i>, providing insights into its genomic characteristics and population dynamics. |
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| ISSN: | 2076-2615 |