The First Genome Survey Sequencing of a Deep-Sea Eel Acromycter nezumi (Asano, 1958) Unveils Its Microsatellite Characteristics and Phylogenetic Implications

In this study, the genome survey of a deep-sea fish Acromycter nezumi (Anguilliformes, Congridae) was conducted to obtain genomic characteristics, identify microsatellite loci, and reconstruct phylogenetic relationships for the first time. Genome size estimation via K-mer approach (K = 17) revealed a haploid genome size of 1627 Mb with 0.67% heterozygosity, 54.73% repetitive sequence ratio, and 43.97% GC content. A total of 1 307 231 microsatellite loci with the length of 11 283 737 bp were identified in the genome by MISA screening. The occurrence frequency and relative abundance were 14.15% and 724.09 loci/Mb. Among the six perfect microsatellites, dinucleotide repeats were the most abundant (916 611, 70.12%), followed by mononucleotide repeats (281 126, 21.51%). Among 1875 motifs, (A)n and (AC)n predominated with the proportions of 41.94 and 30.40%, respectively. The enrichment of type I (≥20 bp, 54.2%) and type II (12–20 bp, 32.1%) microsatellites indicated a high level of polymorphism. Phylogenetic analysis demonstrated that A. nezumi clustered closely with its sibling A. perturbator (bootstrap = 99%), and then grouped with Pseudophichthys splendens, confirming the close evolutionary relationships between them. The results enriched the genomic resource for A. nezumi, provided essential data for future development of molecular markers, genetic mapping, and population diversity studies, as well as offered valuable insights into conservation strategies and adaptive evolution research for deep-sea species.