First Genomic Survey of <em>Pleurocryptella shinkai</em> Provides Preliminary Insights into Genome Characteristics and Evolution of a Deep-Sea Parasitic Isopod
2025
Aiyang Wang | Min Hui | Zhongli Sha
Genomic adaptations of parasitic crustaceans in deep-sea extreme environments are poorly understood. This study presents the first genome survey of <em>Pleurocryptella shinkai</em>, a bopyrid isopod parasitizing deep-sea squat lobsters, using Illumina sequencing. The genome size was estimated to be 1.06 Gb via a <em>K</em>-mer analysis, smaller than its free-living relatives. The repeat content and heterozygosity were 66.31% and 1.14%, respectively, indicating a complex genome. The draft genome assembly yielded 0.93 Gb of scaffolds with an N50 length of 989 bp, and a complete mitochondrial genome of 14,711 bp was obtained. Phylogenetic analyses of 13 mitochondrial protein-coding genes confirmed the monophyly of Bopyridae, supporting <em>Pleurocryptella</em> as the most primitive genus within the group and the key role of deep sea in the origin and diversification of bopyrids. A mitochondrial gene variation analysis identified <em>NAD2</em> and <em>NAD4</em> as promising DNA markers for a population genetic study of <em>P. shinkai</em>. Twenty-four positively selected sites across <em>COX1</em>, <em>NAD2</em>, and <em>NAD4</em> genes in <em>P. shinkai</em> explained the genetic basis of its adaptive evolution at the mitochondrial level. These findings provide valuable genomic resources for deep-sea parasitic crustaceans and establish a foundation for further high-quality genome assembly and adaptive mechanism studies of <em>P. shinkai</em>.
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