Comparative analysis of the complete mitochondrial genomes of three rockfishes (Scorpaeniformes,Sebastiscus) and insights into the phylogenetic relationships of Sebastidae

Abstract

Mitochondrial genome is a powerful molecule marker to provide information for phylogenetic relationships and revealing molecular evolution in ichthyological studies. Sebastiscus species, a marine rockfish, are of essential economic value. However, the taxonomic status and phylogenetic relationships of Sebastidae have been controversial so far. Here, the mitochondrial genomes (mitogenomes) of three species, S. tertius, S. albofasciatus, and S. marmoratus, were systemically investigated. The lengths of the mitogenomes sequences of S. tertius, S. albofasciatus, and S. marmoratus were 16910 bp, 17056 bp, and 17580bp, respectively. It contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and one identical control region (D-loop) among the three species. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by Bayesian Inference (BI) and Maximum Likelihood (ML). Most interestingly, the results indicated Sebastidae and Scorpaenidae were grouped into a separate branch, so the taxonomic status of Sebastidae should be classified into subfamily Sebastinae. Our results may lead to a taxonomic revision of Scorpaenoidei.

Comprehensive Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing

“…Moreover, six Sebastiscus sequences formed a monophyletic group either in the NJ or ML analyses. S. tertius formed a sister group with S. albofasciatus and together had a sister relationship with S. marmoratus, which is consistent with previous studies [8].…”

“…Prior to this study, the genetic information about Sebastiscus was only limited to S. marmoratus and the mitochondrial genome sequences of other Sebastiscus species [8,12,14,15]. In recent years, genomic technology has developed rapidly with the application of NGS technology, which provides an affordable way to solve a wide range of questions [16][17][18].…”

“…Recently, combined with morphological and DNA-barcoding approaches, this species was determined in the Chinese mainland coastal waters as a new record species [7]. Although the external morphology of the S. tertius and S. marmoratus is more similar than S. albofasciatus, recent studies have shown that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level [8]. As a result, it further reveals that the evolutionary relationship of Sebastiscus fishes is necessary to make a deeper comparison and discussion of their genes.…”

Novel gene rearrangement pattern in mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994: new gene order in Encyrtidae (Hymenoptera, Chalcidoidea)

“…In addition, the Ka/Ks of atp8 is as high as 0.9389, which is the highest except for nad2. The high Ka/Ks phenomenon of nad2 and atp8 is also found in other species (Jia et al 2020;Guo et al 2021;Xu et al 2021). The reason for this phenomenon may be that the evolution speed of a gene is related to its function (Wang et al 2011).…”

Complete Mitochondrial Genome of Pseudocaranx dentex (Carangidae, Perciformes) Provides Insight into Phylogenetic and Evolutionary Relationship among Carangidae Family

“…The Mitochondrial genome has become a powerful molecular marker for genetic analysis which can provide additional genetic informative sites and has high conservation and simple structural features [43,44]. Together with the sequences of P. dentex obtained in the present study, the mitochondrial genomes of a total of 36 Carangidae fishes were available.…”