Mitochondrial Genome And Biogeography Of Lefua Costata In China

Lefua costata belonging to Cypriniforme and Nemacheilidae.It is a primary freshwater fish,mainly confining to cold areas in north of the Huai River in China,South Korea,Japan,and eastern Russia.Geographically,its range of distribution is greatly affected by the Pleistocene Ice Age.Firstly,this article analyzed the mitochondrial genome of the Lefua costata,and then analyzed the center of origin and biogeographical process of the genus Lefua based on the entire mitochondrial genome and D-loop region.Based on the mitochondrial Cyt b gene and D-loop,this paper discussed the phylogeography process of Lefua costata in China.The main research results and1.The average mitochondrial genome sequence of Lefua costata is 16 579 bp in length,which contains 2 r RNA genes,22 t RNA genes,13 hydrophobic protein-coding genes,1 non-coding control region(D-loop).Each gene,and the whole genome showed significant A+T base preference.2 r RNAs are 12 S r RNA and 16 S r RNA,12protein-encoding genes,14 t RNA genes are encoded by the H chain;8 t RNAs(Gln,Pro,Ala,Cys,Asn,Glu,Tyr,Ser)and 1 protein encoding gene ND6 is encoded by the L chain.The predicted secondary structure of the 21 t RNA genes is a typical clover structure,2.Based on the mitochondrial genome and D-loop region,origin center and migration of the genus Lefua were analyzed by the phylogenetic ancestral trait reconstruction software RASP(Reconstruct Ancestral State in Phylogenies).The results indicated that the ancestral species of genus Lefua may originate from the eastern part of Russia in the Palaearctic Realm,and Lefua echigonia differentiated at about 23.2284 differentiated and migrated to Honshu and Shikoku Island-related water systems;Lefua costata demographic expansion time at approximately 8.0973(95% HPD:3.3877—12.264)Ma,and gradually migrated to related water systems such as Northeast China and North China,South Korea,Honshu Island,Japan.Finally,the Lefua nikkonis differentiated from the Lefua pleskei;then Lefua nikkonis reached Hokkaido in Japan through the Tatar Strait and Soya Strait,and migrated further south.Lefua pleskei migrated southward in East Asia,it mainly migrated to the border areas of the Russian3.Based on the mitochondrial Cyt b gene and the D-loop region,the genetic diversity and phylogeography of Lefua costata were analyzed on the basis of 272 specimens from 21 sites of 10 basins in north-eastern China.According analysis of mitochondrial Cyt b gene,D-loop region and joint genes,molecular variance analysis(AMOVA),genetic distance(K2P)and genetic differentiation index(FST)between groups showed that the population in Liaodong Peninsula(LD)and other geographic populations have significant differences;the phylogenetic tree and network analysis showed that the haplotypes of 10 water systems are multi-branch and not clustered according to geographical relationship;the haplotypes of 10 water systems are divided into 3 branches: LD population was clustered in branch A,population in Huai-Huang River(HH)and population in Hai-Luan River(HL)were clustered in branch B,branch C contained all geographic populations.The analysis results of D-loop reigon showed that the haplotype diversity and nucleotide diversity of the LD population are the highest(h=0.9158±0.0283,?=0.0257±0.0128);the contribution rate of genetic variation between groups(25.92%)less than the contribution rate of genetic variation within the population(74.08%);according to the average evolution rate(1.00%Ma)of the D-loop sequence of branch B was about 1.5808(95% HPD: 0.4686—3.0695)Ma.Cyt b gene analysis results showed that haplotype diversity and nucleotide diversity of LD populationare were the highest(h=0.9630±0.0118,?=0.0257± 0.0127);the contribution rate of genetic variation between groups(34.88%)less than the contribution rate of genetic variation within the population(65.12%);the divergence time of different geographical populations is evaluated based the fossil calibration points of genus cobitis and genus Triplophysa,the divergence time of branch C and branch B was about 2.1665(95 % HPD:0.6256—3.5668)Ma,branch A and branch(B+C)divergence time was about 2.8239(95% HPD: 1.1630—4.9499)before Ma.The combined analysis of Cyt b gene and D-loop region showed that the haplotype diversity and nucleotide diversity of LD population were the highest(h=0.9869±0.0070,?=0.0189±0.0093);the contribution rate of genetic variation within the population(70.51%)was the main source of variation.Based on the mitochondrial Cyt b gene,D-loop region and the results of the joint genes,they were speculated that the Liaodong Peninsula is one of the origin center of Lefua costata in China and little affected by Quaternary glaciation,other population had beenAccording to the analysis results of mitochondrial genome and D-loop region,the results indicated that the ancestral species of the genus Lefua may originate from the eastern part of Russia in the Palaearctic Realm,and divergence time of Lefua costata was about 8.0973(95% HPD: 3.3877—12.264)Ma and gradually migrated to the northeast region of China.Based on the mitochondrial Cyt b gene and D-loop region,the genetic diversity and phylogeography of Lefua costata distributed in the north of the Huaihe River in China were discussed,they were speculated that the Liaodong Peninsula is one of the origin center of Lefua costata in China and little affected by Quaternary glaciation,gradually formed the distribution pattern of Lefua costata.