Sequencing and analysis of the complete mitochondrial genome of Paracobitis variegatus
SHI Yanru1, XING Lianxi2, CHEN Tao3, YANG Min1, YOU Ping1*
(1 College of Life Science, Shaanxi Normal University, Xi′an 710119, Shaanxi, China;2 College of Life Science, Northwest University, Xi′an 710069, Shaanxi, China;3 Department of Asset Management, Guilin University of Technology, Guilin 541004, Guangxi, China)
Abstract:
The complete mitochondrial genome (mitogenome) sequence of Paracobitis variegatus(Dabry de Thiersant, 1874) was sequenced using the strategy of sub-PCR after long-PCR amplification and annotated.The results showed that the entire mitochondrial genome of P.variegatus is 16 571 bp long with A+T content 55.6﹪.The mitochondrial genome organization of P.variegatus is the same with that in bony fish, which contains 37 genes and 1 control region (named D-loop).The genomic structure is arranged densely, besides D-loop control region, there is only 63 bp intergenic spacer, and 33 bp overlap between genes.Except for COI gene, which uses GTG as the initiation codon, all other protein-coding genes start with the typical ATG codon.The most of 13 protein-coding genes terminated with the typical TAA or TAG codons, while COⅡ, COIII and Cyt b were infered to have an incomplete termination codon T, and ND4 gene terminated with an incomplete termination codon TA.Most tRNA genes could form typical secondary structures except tRNASer(AGN), which had an absence of the DHU arm.The secondary structures of rRNA were predicted.There are 43 helices structures in 12S rRNA, and 6 domains, 53 helices structures in 16S rRNA.In addition, there are 1 terminal associated sequence named TAS1, 3 central conserved sequence blocks named CSB-F, CSB-E and CSB-D, 2 conserved sequence blocks named CSB-2, CSB-3 in the control region of P.variegatus.
KeyWords:
paracobitis variegatus; mitochondrial genome (mtDNA); RNA secondary structure; control region
