A Whole-Genome Survey and the Mitochondrial Genome of Acanthocepola indica Provide Insights into Its Phylogenetic Relationships in Priacanthiformes

<i>Acanthocepola indica</i>, a deep-sea snake fish, is primarily found in the Indo-west Pacific region, including India, Korea, Japan, and the South China Sea. The taxonomic classification of <i>A. indica</i> based on morphological characteristics remains inaccurate and unclear. In this study, we utilized next-generation sequencing to generate comprehensive genomic data for <i>A. indica</i>. The estimated genome size of <i>A. indica</i> was 422.95 Mb, with a heterozygosity ratio of 1.02% and a sequence repeat ratio of 22.43%. Our analysis suggested that <i>A. indica</i> is diploid, and the draft genome assembly consists of 1,059,784 contigs with a contig N50 of 1942 bp. We identified a total of 444,728 simple sequence repeats in the genome of <i>A. indica</i>. Furthermore, we successfully assembled the complete mitochondrial genome (16,439 bp) of <i>A. indica</i>, which included 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Phylogenetic analysis based on mitochondrial genomes revealed that <i>A. indica</i> is closely related to <i>Acanthocepola krusensternii</i> and <i>Cepola schlegelii</i>, providing evidence that the family Cepolidae belongs to the order Priacanthiformes. Population size dynamics analysis indicated that <i>A. indica</i> experienced a bottleneck effect during the Pleistocene Glacial Epoch, likely due to the changes in glacial cycles and sea level fluctuations since ~800 Kya.