Structural characteristics of the control region of the Beaufortia kweichowensis mitochondrial genome

In present study, we identifi ed the structural characteristics of the Beaufortia kweichowensis mtDNA control region using the next-generation sequencing method. Result showed that the control region could be further divided into three parts, including the extended termination associated sequence domain (ETAS), the central conserved domains (CSB-F, CSB-E, CSB-D) and the conserved sequence block domains (CSB-1, CSB-2, CSB-3), and their conserved sequences were identifi ed. Additionally, we found the ETAS domain could be folded and form a 25 bp loop, which are usually considered to play an important role in mtDNA transcript termination. Finally, we reconstructed the phylogenetic relationship among the family of Balitoridae based on the nucleotide sequence of the control region, result showed that the Balitoridae can be divided into two clades, one clade is Gastromyzoninae and the other is Homalopterinae, and the B. kweichowensis was grouped into clade Gastromyzoninae and shared a close relationship with B. szechuanensis. Research Article Structural characteristics of the control region of the Beaufortia kweichowensis mitochondrial genome Gang Wang1, Gui-Hong Chen1, Yu Luo2 and Zheng-Yong Wen1* 1College of Life sciences, Conservation and Utilization of Fishes resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Neijiang Normal University, Neijiang, Sichuan 641100, China 2Institute of Aquaculture, Neijiang Academy of Agricultural Sciences, Neijiang, Sichuan 641000, China Received: 02 July, 2018 Accepted: 12 July, 2018 Published: 13 July, 2018 *Corresponding author: Zheng-Yong Wen, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan 641100, China, Tel: + 86 18582681220; Fax: + 86 18582681220; E-mail:


Introduction
Mitochondrial DNA (mtDNA) is a circular double-strand DNA with a 15-20 kb length in animals, and it usually encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transport RNA (tRNA), and 2 ribosomal RNAs (rRNAs) [1,2]. To date, mtDNA has been widely used for genetic research, taxon classifi cation, phylogenetic evolution research and population studies attribute to its fast variation, maternal inheritance, rapid evolution and lack of recombination [3,4]. Recent years, the mitochondrial genome database growth rapidly following the fast development of high throughput sequencing technology [5], which might provide more chance for scientists to solve the biological mystery in the future.
The control region, also called displacement-loop region (D-loop), is a DNA fragment with fastest evolution rate in mtDNA because it composes of the single strand nucleotide [6].
Fish is one of the most amount groups in vertebrate, and now more than 30000 species has been discovered [11]. Thus far, more than 200 fi sh genome and 1000 fi sh mitochondrial genome has been sequenced and deposited into NCBI database, and these data are available for all researchers, thus then some important scientifi c issue such as the evolutionary relationship of fi sh has been well investigated [12,13], which also will be helpful for species classifi cation and phylogenetic analyses in these groups.
B. kweichowensis (Fang) is an endemic fi sh of the upper reaches of the Beipan River of China, belonging to the family of Balitoridae (Cypriniformes), has not yet been well studied about its phylogenetic evolutionary status [2]. In present study, the structure of control region of B. kweichowensis mtDNA was investigated, and the conserved sequences also was identifi ed.
Subsequently, the phylogenetic tree of the family Balitoridae was reconstructed based on the sequence information of mtDNA control region, which could be helpful to establish the evolutionary status of this species.

Sequencing and structure analysis of control region
The genomic DNA was sequenced using the next-generation sequencing, and then the mitogenome was assembled using B. szechuanensis (GenBank accession number: KP716708.1) as reference. The non-coding control region structure was analyzed and drawn according to the control region structure of other Botiinae fi sh.

Phylogenetic analysis
The phylogenetic tree was constructed with nucleotide sequence of control region using MEGA 6.0 software [14]. The HKY+G model was selected as the best evolutionary model after testing, and the tree was performed using maximum likelihood and bootstrapped with 1000 replications. The species Cycleptus elongatus and Catostomus commersonii were selected as outgroups.

Results and Discussion
The  (Figure 2), which is usually considered to be connection with mitochondria transcript termination [2], and this phenomenon also can be found in other fi shes [15].

Conclusion
The control region of B. kweichowensis could be divided in two three domains, and their conserved sequence were identifi ed. Furthermore, a 25 bp long loop domain was found in the ETAS. Finally, the phylogenetic relationship of the family Balitoridae was analyzed, result highly supported the B. kweichowensis belongs to the subfamily Gastromyzoninae.