Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae

• Published in: Gene Vol. 820; p. 146232
• Main Authors: Wang, Chen, Lai, Tinghe, Ye, Peiyuan, Yan, Yunrong, Feutry, Pierre, He, Binyuan, Huang, Zhongjian, Zhu, Ting, Wang, Junjie, Chen, Xiao
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.04.2022
• Subjects: Duplication remnant; Gene rearrangement; Hemitriakis japanica; Intramitochondrial recombination; Mitogenome; Phylogenetic analyses; Tandem duplication/random loss; Mitogenome; tRNA; PCG; rRNA; BI; Hemitriakis japanica; Duplication remnant; Gene rearrangement; Tandem duplication/random loss; Intramitochondrial recombination; Phylogenetic analyses; ML
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2022.146232

•The first complete mitogenome of the Endangered Japanese topeshark (Hemitriakis japonica).•A novel type of gene rearrangement firstly occurred in shark mitogenome.•The phylogenetic tree showed that Scyliorhinidae, Triakidae and Carcharhinidae were non-monophyletic. In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.