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Molecular Phylogeny of Onychostoma (Cyprinidae) Based on Mitochondrial Genomes

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Molecular Phylogeny of Onychostoma (Cyprinidae) Based on Mitochondrial Genomes 第 42 卷 第 3 期 水 生 生 物 学 报 Vol. 42, No. 3 2018 年 5 月 ACTA HYDROBIOLOGICA SINICA May, 2018 doi: 10.7541/2018.064 MOLECULAR PHYLOGENY OF ONYCHOSTOMA (CYPRINIDAE) BASED ON MITOCHONDRIAL GENOMES ZHANG Chen, CHENG Qi, GENG Hong, LIN Ai-Hua and WANG Hong-Ying (Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China) Abstract: The Onychostoma belongs to cyprinid group and contains 19 species from essentially morphologi- cal classification. However, the molecular phylogenetic relationship of Onychostoma, was not very clear. Here, we presented molecular phylogenetic analysis of 8 species in Onychostoma based on the whole mitochond- rial genome sequence with Danio rerio and Spinibarbus denticulatus as outgroups. The results indicated that Onychostoma did not appear monophyletic which included 3 groups: Onychostoma macrolepis, Ony- chostoma lini and Onychostoma barbatum. O. barbatulum in clade 1, Onychostoma gerlachi and Ony- chostoma simum in clade 2, Onychostoma rara and Onychostoma alticorpus in clade 3. The result was roughly the same as the traditional morphological classification, which divides Onychostoma into three branches. The mitochondrial whole genome was firstly used in Phylogenetic research of Onychostoma and filled the shortage of Phylogenetic studies of this genus. Key words: Mitochondrial DNA; Molecular phylogeny; Onychostoma CLC number: Q959.46+8 Document code: A Article ID: 1000-3207(2018)03-0512-05 Onychostoma is a kind of small freshwater fish replication initiation[3]. Animal mitochondria gene that inhabits mountain streams and rivers in the upper structure is conserved. It is maternal genetic, inde- reaches of rapids. At present, there are 19 nominal pendent in terms of replication, and relatively little re- species in Onychostoma[1]. The species of this genus organization. Therefore, mtDNA has become an ef- widely distributes in the Yellow River, the Yangtze fective tool for the study of phylogeny and popula- River, the Pearl River, and the Red River systems. tion genetics at different levels[4]. To understand the Three species, including O. lini, O. rara, and O. alti- genetic relationship in Onychostoma, we examined corpus, have been listed as endangered fish because mitochondrial DNA of 8 species in Onychostoma and of scarce in number and the narrow distribution analyzed genetic relationship to elucidate the major area[2]. As Onychostoma genius in cyprinid, however, relationship in Onychostoma. Phylogeny had been the molecular phylogenetic relationship in Ony- used extensively for animal and plant classification. chostoma is not clear. The phylogenetic tree of imperial pigeons (Aves: Mitochondrial genome is a closed loop and inde- Columbidae) in the Pacific Ocean using mtDNA and pendent of the nuclear genome. Mitochondrial ge- nuclear sequences was reconstructed. The result nome consists of 13 protein-coding genes, two mito- showed that eastern polynesian endemics were not a chondrial ribosomal rRNA (12SrRNA and 16SrRNA), monophyletic group[5]. Based on nuclear and mtDNA 22 tRNA, and a non-coding region (D-Loop) contain- genes, subgenus Tityus was considered neither sister ing a signal which controls mtDNA transcription and of the remaining species of the genus, nor closely re- Received date: 2017-09-01; Accepted date: 2018-02-06 Foundation item: Supported by the National Natural Science Foundation of China (31001099); the Fundamental Research Funds for the South- central University for Nationalities (CZZ17004) Brief introduction of author: Zhang Chen, E-mail: [email protected] Corresponding author: Wang Hong-Ying, E-mail: [email protected] 3 期 张 晨等: 基于线粒体基因组的白甲鱼属分子系统发育学研究 513 lated to the New World microbuthids with decreasing Posterior probability was used for present repeat credi- neobothriotaxy[6]. New insights into the phylogeny of bility of each branch. Burasaieae (Menispermaceae) with the recognition of 2 Results a new genus and emphasis on the southern Taiwan, China and mainland Chinese disjunction: By combin- 2.1 Sequence features and genetic distance ing cpDNA and ITS data, species of Tinospora are di- The alignments analysis showed that the full- vided into three clades, including a new genus[7]. length mitochondrial DNA of these 8 species ranged from 16589 to 16607 bp. The average content propor- 1 Material and methods tions of A, T, C, and G were 31.3%, 24.4%, 28.2%, 1.1 Taxon selection and 16.1% respectively. The sum of the content pro- 8 species of Onychostoma which already have portion of A+T (55.7%) was higher than that of C+G the whole mitochondrial DNA sequences were selec- (44.3%). This was consistent with range of GC in ver- [13] ted. All the mtDNA sequences were downloaded tebrates . MtDNA of Onychostoma appeared strong from GenBank. GenBank accession numbers of each base composition bias and guanine was lower than species were listed in Tab. 1. other three bases. There were 16655 bp length after 1.2 Data analysis alignments. All the whole mtDNA sequences were used as Based on Kimura two-parameter model, we de- multiple comparison by Clustal W[8]. Coding se- termined the genetic distance to define genetic differ- quences were translated into amino acids by entiation in the taxon. The results showed that the ge- MEGA5.0[9]. Sequences of genetic distance and the netic distances in the genus of Onychostoma ranged content of each nucleotide variation were also ana- from 0.004 to 0.118, while the distances between lyzed by MEGA5.0. Genetic distance between two Onychostoma and outgroups ranged from 0.140 to species was calculated with Kimura two-parameter 0.282 (Tab. 2). model. Neighbor-Joining method (NJ), Maximum Individual sequence transition and transversion Likelihood method (ML), and Bayesian Inference values were shown as a linear relationship and unsa- method (BI) were used in establishing phylogenetic turated (Fig. 1). It also showed phylogenetic signifi- [14] trees. ML tree and NJ tree were established by cance and could be used for data analysis . At the MEGA5.0[9] and BI tree was established by level of variation, the number of transition was signi- MrbayesV3.2.5[10]. DAMBE was used for sequence ficantly more than that of transversion. The range of substitution analysis. Both in NJ and ML, the number the ratio of transition and transversion of the se- of nonparametric bootstrap replications was set as quences was from 3.075 to 15.205 and the average 1000. The GTR+I+G model was chosen by MOD- value was 5.787. ELTEST3.7[11, 12] as the best fit model for the BI 2.2 Molecular phylogenetic trees method. The Markov Chain Monte Carlo (MCMC) NJ, ML, and BI methods were used in phyloge- process in Mrbayes was conducted for 100 million netic analysis of mtDNA sequence of 8 Onychostoma. generations. For every 1000 steps, the initial 250 Danio rerio and Spinibarbus denticulatus were used sampled data were discarded as burin-in. The 4 chains as outgroups. The trees from three methods were si- include 3 heating chains (temp 0.5) and 1 cold chain. milar while O. Barbatulum was identical in NJ and ML trees but it was different in BI tree (Figs. 2—4). Tab. 1 Species and their mtDNA genome sequences used in this In NJ and ML method, O. rara and O. alticorpus study were sister groups at the base, suggesting they were rela- Family Genus Species GenBank No. tively primitive in evolution. Meanwhile, O. simum Cyprinidae Onychostoma O. alticorpus KC791686 and O. gerlachi were in the sister groups while O. Cyprinidae Onychostoma O. barbatulum KC896762 lini, O. barbatum, O. macrolepis, and O. barbatulum Cyprinidae Onychostoma O. barbatum KT438512 were in monophyletic groups (with a bootstrap value Cyprinidae Onychostoma O. gerlachi KP244449 99 in ML and 86 in NJ). According to the NJ and ML Cyprinidae Onychostoma O. lini JQ343982 tree, Onychostoma was divided into 3 taxa: O. rara+O. alticorpus, O. simum+O. gerlachi and O. Cyprinidae Onychostoma O. macrolepis KF999680 lini+O. barbatum+O .macrolepis+O. barbatulum Cyprinidae Onychostoma O. rara KF626377 (Fig. 2 and 3). Cyprinidae Onychostoma O. simum KF021233 The topologies of the NJ tree and the ML tree Cyprinidae Danio D. rerio AC024175 were similar with only difference in bootstrap and Cyprinidae Spinibarbus S. denticulatus KC852197 Bayesian posterior probability (BPP) value. The posi- 514 水 生 生 物 学 报 42 卷 Tab. 2 Genetic distance between two species based on Kimura two-parameter model D. rerio S. denticulatus O. alticorpus O. barbatulum O. barbatum O. gerlachi O. lini O. macrolepis O. rara O. simum D. rerio S. denticulatus 0.265 O. alticorpus 0.282 0.141 O. barbatulum 0.281 0.147 0.118 O. barbatum 0.275 0.141 0.105 0.099 O. gerlachi 0.278 0.147 0.115 0.111 0.106 O. lini 0.275 0.140 0.105 0.095 0.026 0.102 O. macrolepis 0.277 0.141 0.107 0.100 0.030 0.106 0.026 O. rara 0.274 0.136 0.091 0.108 0.097 0.110 0.095 0.097 O. simum 0.281 0.149 0.117 0.113 0.108 0.004 0.105 0.108 0.112 0.10 O. lini R 48 0.09 ² = 0.9946 100 O. macrolepis 0.08 99 O. barbatum Clade1 0.07 86 O. barbatulum 0.06 O. gerlachi 100 Clade2 0.05 100 O. simum O. alticorpus 0.04 100 O. rara Clade3 R² = 0.9359 0.03 S. denticulatus 0.02 D. rerio Outgroup 0.01 Transition and stransversion Transition 0.00 0.01 0.00 0.02 0.04 0.06 0.08 0.10 0.12 p-distance Fig.
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