Sequencing and Structural Characteristics Analysis of Mitochondrial Genome in Rhodeus ocellatus from Ou River
LIU Kai1,*, FENG Xiao-Yu1, WU Yan-Qin2, CHU Tian-Jiang1, XIE Nan1
1 Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China; 2 Lishui Aquatic Product Technology Promotion Department, Lishui 323000, China
Abstract:Rhodeus ocellatus is a kind of ornamental fish with a fair market prospect due to its bright color and beautiful body. The sequencing and analysis of the mitochondrial genome (mtGenome) of R. ocellatus, and the exploration of mtGenome differences of R. ocellatus from different geographical populations and the phylogenetic position of R. ocellatus in Acheilognathinae subfamily at the mtGenome level are of great significance for the phylogenetic study of R. ocellatus. In this study, PCR amplification, sequencing, and software splicing were used to obtain the complete mtGenome of R. ocellatus from Ou River. The full-length sequence (GenBank No. MW007386) was 16 675 bp, and the base composition was A (28.98%), G (17.09%), C (26.51%), and T (27.42%). There were 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs. The (A+T) content of the mtGenome and PCGs in the mtGenome of R. ocellatus from Ou River was 56.41% and 56.27%, respectively. Both mtGenome and PCGs had noticeable AT preference. The 22 tRNAs, except tRNA-Ser(AGY), had a typical clover structure. Based on BLAST alignment, the sequence identity of R. ocellatus from Ou River was 83.84% with that of R. ocellatus from Dong River, 95.07% with that of R. ocellatus from Japan, 93.11% with that of R. ocellatus with GenBank No. DQ026430, 99.03% with that of Acanthorhodeus chankaensis from Tumen River, 83.72% with that of A. chankaensis from Heilong River, and 83.84% with that of A. chankaensis from Yuan River. In addition, the genetic distance between R. ocellatus from Ou River and A. chankaensis from Tumen River was the closest, followed by R. ocellatus from Japan, and R. ocellatus from Ou River was farther away. Phylogenetic tree was constructed based on complete mtGenomes of 25 species of Acheilognathinae subfamily belonging to 3 genera. R. ocellatus from Ou River was closely related to A. chankaensis from Tumen River, but was relatively distant to R. ocellatus from Dong River. The present study provides reference for the genetic diversity protection and breeding of R. ocellatus from Ou River.
[1] 连总强, 滚双宝, 李力, 等. 2017. 基于第二代测序技术兰州鲇线粒体基因组全序列测定与分析[J]. 水生生物学报, 41(2): 334-345. (Lian Z Q, Gun S B, Li L, et al.2017. Sequencing and analysis of the complete mitochondrial genome of Silurus lanzhouensis based on next generation sequencing technologies[J]. Acta Hydrobiologica Sinica, 41(2): 334-345.) [2] 廖彩萍, 曾燏, 唐琼英, 等. 2013. 高体鳑鲏的性选择问题研究[J]. 水生生物学报, 37(6): 1112-1117. (Liao C P, Zeng Y, Tang Q Y, et al.2013. The sexual selection of the rose bitterlings Rhodeus ocellatus[J]. Acta Hydrobiologica Sinica, 37(6): 1112-1117.) [3] 刘凯, 冯晓宇, 马恒甲, 等. 2020. 钱塘江三角鲂线粒体基因组测序及结构特征分析[J]. 浙江农业学报, 32(9): 1591-1608. (Liu K, Feng X Y, MA H J, et al.2020. Complete sequence and gene organization of the mitochondrial genome of Megalobrama terminalis from Qiantang River[J]. Acta Agriculturae Zhejiangensis, 32(9): 1591-1608.) [4] 毛明光, 顾杰, 刘瑞婷, 等. 2019. 太平洋鳕线粒体全基因组测序及结构特征分析[J]. 水生生物学报, 43(1): 17-26. (Mao M G, Gu J, Liu R T, et al.2019. Analysis of complete mitochondrial genome sequences of Gadus Macrocephalus[J]. Acta Hydrobiologica Sinica, 43(1): 17-26.) [5] 史宝, 柳学周, 刘永山, 等. 2019. 黄条鰤线粒体全基因组测序及结构特征分析[J]. 中国水产科学, 26(3): 405-415. (Shi B, Liu X Z, Liu Y S, et al.2019. Complete sequence and gene organization of the mitochondrial genome of Seriola aureovittata[J]. Journal of Fishery Sciences of China, 26(3): 405-415.) [6] 孙博, 常玉梅, 苏宝锋, 等. 2018. 黑龙江流域3种鳑鲏属鱼类的DNA条形码分析[J]. 基因组学与应用生物学, 37(12): 5220-5225. (Sun B, Chang Y M, Su B F, et al.2018. DNA barcoding analysis of three rhodeus fishes in Heilongjiang River[J]. Genomics and Applied Biology, 37(12): 5220-5225.) [7] 夏继刚, 刘香, 黄艳. 2019. 高体鳑鲏化学预警响应与“个性”行为的关联[J]. 生态学报, 39(17): 6425-6432. (Xia J G, Liu X, Huang Y.2019. The link between chemical alarm cue-induced behavioral responses and personality in Rhodeus ocellatus[J]. Acta Ecologica Sinica, 39(17): 6425-6432.) [8] 杨秀平, 刘焕章, 唐治军. 2002. 高体鳑鮍(Rhodeus ocellatus (kner))的形态变异及地理分化研究[J]. 湖北大学学报(自然科学版), 24(2): 173-177. (Yang X P, Liu H Z, Tang Z J.2002. Morphological and geographical differentiations of Rhodeus ocellatus[J]. Journal of Hubei University (Natural Science Edition), 24(2): 173-177.) [9] 杨泽民, 谢数涛, 章群, 等. 2012. RNA二级结构预测及其在分子分类研究中的应用[J]. 安徽农业科学, 40(7): 3919-3922, 3944. (Yang Z M, Xie S T, Zhang Q.2012. Prediction and application of RNA secondary structure in the study of molecular taxonomy[J]. Journal of Anhui Agricultural Sciences, 40(7): 3919-3922, 3944.) [10] 钟东, 赵贵军, 张振书, 等. 2002. 基因组内碱基分布整体均衡与局部不均衡的研究进展[J]. 遗传, 24(3): 351-355. (Zhong D, Zhao G J, Zhang Z S, et al.2002. Advance in the entire balance and local unbalance of base distribution in genome[J]. Hereditas, 2002, 24(3): 351-355.) [11] 周传江, 马爱喆, 汪曦, 等. 2019. 鱼类线粒体基因组研究进展[J]. 河南师范大学学报(自然科学版), 47(2): 74-82. (Zhou C J, Ma A Z, Wang X, et al.2019. Progress on fish mitochondrial genome[J]. Journal of Henan Normal University (Natural Science), 47(2): 74-82.) [12] 朱世华, 郑文娟, 邹记兴, 等. 2007. 鲹科鱼类线粒体DNA控制区结构及系统发育关系[J]. 动物学研究, 28(6): 606-614. (Zhu S H, Zheng W J, Zou J X, et al.2007. Mitochondrial DNA control region structure and molecular phylogenetic relationship of Carangidae[J]. Zoological Research, 28(6): 606-614.) [13] Altschul S F, Madden T L, Schäffer AA, et al.1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs[J]. Nucleic Acids Research, 25(17): 3389-3402. [14] Cannone J J, Subramanian S, Schnare M N, et al.2002. The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs[J]. BMC Bioinformatics, 3: 2. [15] Chen C, Chen H, Zhang Y, et al.2020. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 13(8): 1194-1202. [16] Comeron J M, Aguadéo M.1998. An evaluation of measures of synonymous codon usage bias[J]. Journal of Molecular Evolution, 47(3): 268-274. [17] Fernández-Silva P, Enriquez J A, Montoya J.2003. Replication and transcription of mammalian mitochondrial DNA[J]. Experimental Physiology, 88(1): 41-56. [18] Grant J R, Arantes A S, Stothard P.2012. Comparing thousands of circular genomes using the CGView Comparison Tool[J]. BMC Genomics, 13(1): 1-8. [19] Guo X, Liu S, Liu Y.2003. Comparative analysis of the mitochondrial DNA control region in cyprinids with different ploidy level[J]. Aquaculture, 224(1-4): 25-38. [20] He S, Gu X, Mayden R L, et al.2008. Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome[J]. Molecular Phylogenetics and Evolution, 47(1): 419-425. [21] Hixson J E, Wong T W, Clayton D A.1986. Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication[J]. The Journal of Biological Chemistry, 261(5): 2384-2390. [22] Hoang D T, Chernomor O, Haeseler von A, et al.2018. UFBoot2: Improving the ultrafast bootstrap approximation[J]. Molecular Biology and Evolution, 35(2): 518-522. [23] Hu J, Chen Y, Zhao H, et al.2016. Complete mitochondrial genome of Rhodeus ocellatus (Cypriniformes: Cyprinidae)[J]. Mitochondrial DNA, 27(5): 3489-3490. [24] Hyvärinen A K, Pohjoismäki J L O, Reyes A, et al.2007. The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA[J]. Nucleic Acids Research, 35(19): 6458-6474. [25] Iwasaki W, Fukunaga T, Isagozawa R, et al.2013. MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline[J]. Molecular Biology and Evolution, 30(11): 2531-2540. [26] Kumar S, Stecher G, Li M, et al.2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 35(6): 1547-1549. [27] Lee W J, Conroy J, Howell W H, et al.1995. Structure and evolution of teleost mitochondrial control regions[J]. Journal of Molecular Evolution, 41(1): 54-66. [28] Lowe T M, Chan P P.2016. tRNAscan-SE On-line: Integrating search and context for analysis of transfer RNA genes[J]. Nucleic Acids Research, 44(W1): W54-W57. [29] Lv W, Cao D, Wu J, et al.2015. The complete mitochondrial genome sequence of Khanka spiny bitterling (Acanthorhodeus chankaensis)[J]. Mitochondrial DNA, 26(6): 842-843. [30] Nguyen L, Schmidt H A, von Haeseler A, et al.2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies[J]. Molecular Biology and Evolution, 32(1): 268-274. [31] Nomenclature Committee for the International Union of Biochemistry (NC-IUB). 1985. Nomenclature for incompletely specified bases in nucleic acid sequences[J]. European Journal of Biochemistry, 150(1): 1-5. [32] Okonechnikov K, Golosova O, Fursov M.2012. Unipro UGENE: A unified bioinformatics toolkit[J]. Bioinformatics, 28(8): 1166-1167. [33] Polacek N, Mankin A S.2005. The ribosomal peptidyl transferase center: Structure, function, evolution, inhibition[J]. Critical Reviews in Biochemistry and Molecular Biology, 40(5): 285-311. [34] Rozov A, Demeshkina N, Khusainov I, et al.2016. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code[J]. Nature Communications, 7: 10457. [35] Rozas J, Ferrer-Mata A, Sánchez-DelBarrio J C, et al.2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Molecular Biology and Evolution, 34(12): 3299-3302. [36] Saitoh K, Sado T, Mayden R L, et al.2006. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences[J]. Journal of Molecular Evolution, 63(6): 826-841. [37] Sato N S, Hirabayashi N, Agmon I, et al.2006. Comprehensive genetic selection revealed essential bases in the peptidyl-transferase center[J]. Proceedings of the National Academy of Sciences of the USA, 103(42): 15386-15391. [38] Satoh T P, Miya M, Mabuchi K, et al.2016. Structure and variation of the mitochondrial genome of fishes[J]. BMC Genomics, 17(1): 1-20. [39] Sbisà E, Tanzariello F, Reyes A, et al.1997. Mammalian mitochondrial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications[J]. Gene, 205(1/2): 125-140. [40] Seutin G, Lang B F, Mindell D P, et al.1994. Evolution of the WANCY region in amniote mitochondrial DNA[J]. Molecular Biology and Evolution, 11(3): 329-340. [41] Sharp P M, Li W H.1986. An evolutionary perspective on synonymous codon usage in unicellular organisms[J]. Journal of Molecular Evolution, 24(1/2): 28-38. [42] Stothard P, Wishart D S.2005. Circular genome visualization and exploration using CGView[J]. Bioinformatics, 21(4): 537-539. [43] Tan J, Yin Z, Huang H, et al.2019. Characterization and phylogenetic analysis of Acheilognathus chankaensis mitochondrial genome[J]. Mitochondrial DNA Part B, 4(1): 1148-1149. [44] The RNAcentral Consortium.2019. RNAcentral: A hub of information for non-coding RNA sequences[J] (published correction appears in Nucleic Acids Research, 47(D1): D1250-D1251). Nucleic Acids Research, 47(D1): D221-D229. [45] Wolstenholme D R, Jeon K W.1992. Mitochondrial Genomes[M]. San Diego, Academic Press, pp. 173-216. [46] Wright F.1990. The 'effective number of codons' used in a gene[J]. Gene, 87(1): 23-29. [47] Xu H, Yang P, Dai W, et al.2020. Sequence characterization and phylogenetic analysis of mitogenome of the Acanthorhodeus chankaensis Dybowsky from Cao'e River[J]. Mitochondrial DNA Part B, 5(1): 545-547. [48] Yan J, Liu L, Liu S, et al.2010. Comparative analysis of mitochondrial control region in polyploid hybrids of red crucian carp (Carassius auratus) × blunt snout bream (Megalobrama amblycephala)[J]. Fish Physiology and Biochemistry, 36(2): 263-272. [49] Zhao J L, Wang W W, Li S F, et al.2006. Structure of the mitochondrial DNA control region of the Sinipercine fishes and their phylogenetic relationship[J]. Acta Genetica Sinica, 33(9): 793-799. [50] Zuker M.2003. Mfold web server for nucleic acid folding and hybridization prediction[J]. Nucleic Acids Research, 31(13): 3406-3415.