Analysis Of Mitochondrial Genome Characteristics In Some Cartilaginous Fishes And Identification Of Cox1 Gene

Cartilaginous fish is the most primitive jaws,including the chimaera of Holocephali and the shark and ray of Elasmobranchii.The cartilaginous fish which is numerous and widely distributed not only has a special evolutionary status in vertebrate phylogeny,its scientific research and economic value are also very prominent.Because of its special living environment,sample collection and research are relatively difficult.Although the species of the cartilaginous fish are abundant and its biological value and economic value are very high,related research reports especially the systematic research are still relatively few.This research is based on the existing GenBank data of the cartilaginous fish mitochondrial genome,analyzing the characteristics of the mitochondrial genome of some cartilaginous fishes in China,in order to understand the basic characteristics of the cartilaginous fish in the mitochondrial genome and analyze the phylogenetic relationships among cartilaginous fishes to screen the DNA barcoding gene suitable for the identification of the cartilaginous fish.At the same time,we collected muscle samples of cartilaginous fishes from Fujian.Guangdong,Zhejiang and Shandong provinces and got mitochondrial cox 1 gene fragment by DNA sequencing to analyse the sequence characteristics and verify its feasibility of the identification of cartilaginous fishes.The results are as follows:1.Analysis of mitochondrial genome characteristics of 50 cartilaginous fishes:(1)Different from the inverted or ectopic phenomenon in echinoderms,the arrangement of mitochondrial genes in the cartilaginous fish conforms to the general coding characteristics of vertebrates.(2)The average content of A + T(60.64%)is higher than that of G + C(39.36%),and there is a significant base bias.Its average content of A + T is also higher than that of teleost fish,which is consistent with the results of previous studies.(3)cox 1 gene has the lowest proportion of different loci and nad5 gene has the largest number of different loci,it is speculated that cox 1 gene can be used as an ideal DNA barcoding gene for the identification of cartilaginous fishes and nad 5 gene can be used as an auxiliary marker of cox 1 gene.2.Phylogenetic tree based on the construction of 13 protein genes of the mitochondrial genome of the cartilaginous fish display:(1)The individual species of cartilaginous fishes are clustered into monophyletic clades at the level of the order,which provides molecular evidence for morphological classification of cartilaginous fishes.(2)The topology of the phylogenetic tree shows that cartilaginous fishes are divided into two large branches Holocephali and Elasmobranchii.The topology of phylogenetic tree is a preliminary verification of the classification at the level of the order of the cartilaginous fishes in the traditional taxonomy.(3)Phylogenetic relationships of cartilaginous fishes:(((((Carcharhiniformes + Lamniformes)+Orectolobiformes)+ Heterodontiformes)+((Squaliformes + Pristiophoriformes)+Squatiniformes))+(Rajiformes + Myliobatiformes))+ Chimaeriformes.3.Collecting the muscle samples of Rhincodon typus,Sphyrna lewini and Squalus suckleyi to extract mitochondrial cox 1 gene fragment,this study found:(1)Intraspecific genetic difference is larger in cox 1 gene fragments of Sphyrna lewini,and has overlap in genetic distance between intraspecific and interspecific.So it is speculated that there may be errors in the species identification of cox 1 gene.Because of the influence of the geographical environment,the genetic diversity of some species is larger,and has overlap in genetic distance between intraspecific and interspecific,which affects the accuracy of molecular identification.(2)Phylogenetic analysis based on twenty species:In addition to Squatina.formosa and Squatina nebulosa,the other eighteen cartilaginous fishes are existed as monophyletic in NJ tree.Based on the analysis of the characteristics of mitochondrial genome and the feasibility of cox 1 gene in identification of the cartilaginous fish in China,this paper puts forward the following viewpoints and conclusions as follows:(1)Speculated that cox 1 gene can be used as an ideal DNA barcoding gene for identification of the cartilaginous fish and nad 5 gene can be used as an auxiliary marker of cox 1 gene.(2)It verifis the traditional classification rules of cartilaginous fishes on the large taxonomic level.(3)The feasibility of cox 1 gene in molecular identification of the cartilaginous fish is preliminarily verified.(4)There are some errors in the identification of cox 1 gene in the widely distribution species and closely related species of cartilaginous fish,and it is speculated that the single cox 1 gene might reduce the accuracy of molecular identification of cartilaginous fishes.