Structure, evolution and phylogenetic informativeness of eelpouts (Cottoidei: Zoarcales) mitochondrial control region sequences

Abstract

Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales). To achieve this, we carried out a comparative phylogenetic and structural analysis of 29 CR sequences belonging to the long shanny Stichaeus grigorjewi together with nine sequences of other eelpouts taxa representing four families in contrast to mitochondrial protein-coding fragments. The CR organization within S. grigorjewi, as well as in all other eelpouts, is consistent with the common three-domain structure known from most vertebrates. We found a hidden CR variation constrains on the landscape level and a lack of nucleotide saturation. Finally, our results demonstrate the advantage of the length variation in CR sequences for phylogenetic reconstructions among eelpouts.

The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

“…As the ‘second genome’ of eukaryotes, mitochondrial genome plays an important role in aging, death, disease occurrence and stress resistance of eukaryotes 54 – 56 . Mitochondrial genome organization, core protein coding genes, repetitive sequences, gene arrangement, the number and structure of tRNAs, and open reading frames provided rich genetic information for understanding the genitics and evolution of eukaryotes 57 – 59 . Mitochondrial genomes have been extensively studied in animals.…”

Complete mitochondrial genome of Stichaeus nozawae Jordan & Snyder 1902 (Zoarcales: Stichaeidae)

“…Shedko 2017). On the other hand, the mitochondrial control region (CR) sequences of eelpouts demonstrate the lack of saturation compared to protein-coding genes (Turanov, Lee, et al 2019) and, therefore, it might express the natural patterns of evolutionary constrains of mitochondrial genome (mitogenome). To approach this problem from the genomic point of view, we obtained the first sequence of mitogenome for SN and compared with the mitogenome of SG .…”

Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species

“…Moreover, there were 25 variable sites in 22 tRNAs, 113 variable sites in the D-loop, and 291 variable sites in 13 PCGs ( Table 4 ). A previous study reported that the control region is a non-coding sequence in mtDNA, it possesses relatively low selection pressure during evolution, and it has greater polymorphism than other mitochondrial elements [ 58 ]. Among all mitochondrial elements, the D-loop, nad3 , nad4l , nad6 , and atp8 contained a higher percentage of variable sites than other elements.…”