Characterization and phylogenetic implications of newly sequenced mitochondrial genomes of cobitid fish Acantopsis Rungthipae (Boyd, Nithirojpakdee & Page, 2017).

Abstract

Background: Acantopsis rungthipae has significant ornamental and ecological value. This study aimed at structurally characterizing the A. rungthipae mitochondrial genome and elucidate its phylogenetic position in Cobitidae.

Methods and results: High-throughput sequencing technology was used to obtain the complete sequence of the mitochondrial genome of A. rungthipae and reconstruct a Cobitidae phylogenetic tree based on the sequence of 13 protein-coding genes. The entire mitochondrial genome of A. rungthipae was 16,600 bp, containing 22 tRNA genes, 13 protein-coding genes, 2 rRNAs, and 2 non-coding regions (D-loop and OL). The base composition showed a significant AT preference, with the highest A + T content (67.1%) in the D-loop region. Among the protein-coding genes, 12 had ATG as a typical starting codon, while only COXI had GTG as a special starting codon. Twenty-one of the tRNA genes exhibited clover structure, and only tRNA-Ser (GCT) could not fold into a clover structure because of the absence of DHU arms. The phylogenetic tree was reconstructed using the Bayesian and maximum likelihood methods and showed that A. rungthipae and Acantopsis choirorhynchos converged into one branch, and their phylogenetic relationships were relatively close.

Conclusions: Our findings supplement basic data on the A. rungthipae mitochondrial genome and deepen the understanding of the evolutionary relationships of the genus Acantopsis. Clarifying the evolutionary relationships between different species in Acantopsis lays a solid foundation for subsequent research on fish adaptation and selection pressure.