First Genomic Survey of Pleurocryptella shinkai Provides Preliminary Insights into Genome Characteristics and Evolution of a Deep-Sea Parasitic Isopod

Genomic adaptations of parasitic crustaceans in deep-sea extreme environments are poorly understood. This study presents the first genome survey of Pleurocryptella shinkai, a bopyrid isopod parasitizing deep-sea squat lobsters, using Illumina sequencing. The genome size was estimated to be 1.06 Gb via a K-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 Pleurocryptella 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 NAD2 and NAD4 as promising DNA markers for a population genetic study of P. shinkai. Twenty-four positively selected sites across COX1, NAD2, and NAD4 genes in P. shinkai 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 P. shinkai.