Complete Mitochondrial Genome Sequencing Of Leuciscus Idus And Phylogenetic Analysis Of Subfamily Leuciscinae

Leuciscus idus is a cold water fish, distributed in Europe, Central Asia and the Irtysh River in northern Xinjiang. L. idus is a fish of Leuciscus. There exist about more than30species in Leuciscus in the world, and seven species in China; they are Leuciscus waleckii, Leuciscus waleckii tumensisi, Leuciscus merzbacheri, Leuciscus leuciscus baicalensis, Leuciscus idus, Leuciscus brandti, Leuciscus hakonensis. In recent years, nearly all species’ populations of Leuciscus is decreased in the number and scale, some species have already disappeared before people begin to realize them. In2013, an article of the Economic Observer reported reported that Leuciscus chuanchicus had disappeared in the Yellow River, the situation of the fishes belonging to Leuciscus in our country is evident. Currently, the mitochondrial genetic information of Leuciscus fishes has been made public isn’t a lot, so far GenBank has only released the whole mitochondrial gene sequence of L. waleckii. In this experiment, using the mitochondrial gene of L. waleckii as a template, we use the primer walking method to amplify and detect the whole mitochondrial gene sequence of L. idus and then upload it to GenBank, which can enrich the Leuciscus data of mitochondrial genome and provide reference and support for the research of Leuciscus mitochondrial genes as well as other related species.Subfamily Leuciscinae belongs to Cypriniformes Cyprinidae. Cyprinidae fish, as the biggest extant families in the world, their phylogenetic relationships, origins of the distribution, population differences have become the focus of research. Subfamily Leuciscinae as its subordinate taxa, naturally attracts people’s favor. For example, Danio rerio has become a model organism for vertebrate developmental biology research. In this study, according to Wu Xianwen’s classification of Subfamily Leuciscinae in Chinese Cyprinid Fishes, we download the mitochondrial genetic information of16species belonging to16genera of Subfamily Leuciscinae which had been announced in GenBank. In combination with the mitochondrial genetic information of L. idus obtained in this study, we built the phylogenetic evolutionary tree of subfamily Leuciscinae from the perspective of the Cyt b and16S rRNA genes. In this dtudy, we preferred Kimma2-Pamameter diatance model of neighbor-joining and maximum likelihood method to construct NJ and ML tree; we chose GTR+Γ+I model of Bayesian inference method to construct BI tree. The main conclusions are as follows:1.The full length of the complete mitogenome of L. idus is16603bp and its similarity with the sequence of L. waleckii is92.1%. The orientation and arrangement of genes on the DNA chain are similar to most other sequenced fish mitochondrial DNAs. Mitochondrial genes have a high utilization of the bases:extremely tight gene sequencing, little genetic interval between genes and even some gene overlaps. Sequences encoding proteins have no introns. AT content percentage of the whole sequence is55%, expressed as AT bias. The protein coding sequence, rRNA sequences, tRNA sequences and sequences of the control region all show AT bias, in which the control region shows the maximum AT content of63.8%. Among the13protein-coding sequences, CO I gene is initiated with a GTG codon, while the others use ATG as their start codon. ND1, CO1, ATPase6, ND4L and ND5genes use TAA as their stop codon, while ATPase8and ND6genes’is TAG, and the rest ones end up with incomplete stop codons T or TA.2.The similarity of the six Phylogenetic relationship trees, which were constructed based on Cyt b and16S rRNA genes using the neighbor-joining method, the maximum likelihood method and the Bayesian inference method, was high, and the difference between them was mainly appeared in the position of genera Ctenopharynodon, Mylopharyngodon and Spualiobarbus. In the NJ tree of Cyt b gene, genera Mylopharyngodon and Spualiobarbus was a sister group to each other, and the monophyletic group they formed formed a sister group relationship with genera Ctenopharynodon again. But in the ML tree of Cyt b gene, the position of Ctenopharynodon and Mylopharyngodon interchanged. In the BI tree of Cyt b gene, genera Mylopharyngodon was a sister group with the monophyletic group formed by genera Opsariichthys and Zacco, and that together again formed a sister group relationship with genera Ctenopharynodon and Spualiobarbus mutually. In the ML tree of16S rRNA gene, the relationship between genera Spualiobarbus and Ctenopharynodon was closer. However, in the NJ tree of16S rRNA gene, genera Spualiobarbus had a closer genetic relationship with genera Mylopharyngodon. In the BI tree of16S rRNA gene, the branch constituted by genera Spualiobarbus, Ctenopharynodon and Mylopharyngodon was no longer at the top of the tree, but closer to the root of the tree.