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

Simple Summary: In this study, we explored the genetic characteristics and evolutionary history of Acanthocepola indica, a deep-sea snake fish. Genome sequencing revealed that A. indicais a diploidspecies with high heterozygosity and many repetitive sequences. We identified over 400,000 simple sequence repeats, which may serve as valuable markers for future genetic research. Additionally, we assembled the fish's mitochondrial genome, uncovering important genes and patterns associated with amino acid production. Our analysis also showed that A. indicahas experienced populationdeclines, likely due to sea level changes during the Pleistocene Glacial Epoch. These findings lay the ground work for further research on this species' adaptation to deep-sea environments and support conservation efforts. Acanthocepola indica, 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 A. indica based on morphological characteristics remains inaccurate and unclear. In this study, we utilized next-generation sequencing to generate comprehensive genomic data for A. indica. The estimated genome size of A. indica was 422.95 Mb, with a heterozygosity ratio of 1.02% and a sequence repeat ratio of 22.43%. Our analysis suggested that A. indica 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 A. indica. Furthermore, we successfully assembled the complete mitochondrial genome (16,439 bp) of A. indica, which included 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Phylogenetic analysis based on mitochondrial genomes revealed that A. indica is closely related to Acanthocepola krusensternii and Cepola schlegelii, providing evidence that the family Cepolidae belongs to the order Priacanthiformes. Population size dynamics analysis indicated that A. indica experienced a bottleneck effect during the Pleistocene Glacial Epoch, likely due to the changes in glacial cycles and sea level fluctuations since similar to 800 Kya.