Complete Mitochondrial Genome Analysis And Phylogeny Of Turtles

As early as the late Triassic,200 million years ago,when giant dinosaurs roamed the land,there were signs of turtles.According to the Reptile-Database,361 species of turtles have been documented and named.Their habitats have been destroyed by humans,and for a variety of reasons,such as for food or as pets,the poor turtles cannot escape the fate of rampant hunting.It is also urgent to protect the germplasm resources of turtles.Therefore,it is necessary for humans to conduct in-depth research on turtles,including but not limited to further understanding of the phylogenetic relationship and species classification of turtles.The typical vertebrate mitochondrial genome is a covalently closed double stranded circular DNA with a total length of about 16kb-20 kb.The mitochondrial genome is relatively superior to the nuclear genome because of its simple structure,maternal inheritance and less gene rearrangement,so it is regarded as the key research object in the research of animal genetic evolution and phylogenetic relationship.Up to now(March 2021),there are 132 species in the complete mitochondrial genomes of turtles officially published by NCBI,which means that far more than half of turtles have not been measured by human beings.In the order of turtles,the largest number of species is geochelidae.However,only 36 of the 71 species were found to have complete mitochondrial genomes.Obviously,we still need to do a lot of work to study the phylogenetic relationship of turtles using mitochondrial genome data.In this study,the complete mitochondrial genome of geoemyda spengleri was obtained,and its amino acid composition,synonymous codon usage preference and other parameters were statistically analyzed.The total length of mitochondrial genome is 17448 BP,with 38 genes.Among them,23 t RNAs are more than typical vertebrate mitochondrial genome,including one t RNA Glu pseudogene,13 protein coding genes(PCGs),two r RNAs and one D-loop region.Its genome structure,gene sequence and base composition are slightly different from those of typical vertebrates.Genetic rearrangement exists and evolutionary hypothesis is proposed.There was an extra g insertion at site 215 of nadh3 gene.Three conserved sequence frames(csb1-3)were found near the 5 ’end of the control region,and a long tandem repeat(repeat 3 times)with a motif of 23 BP(attattattaatc)was found at the 5’ end of the control region.Based on the mitochondrial genome sequences of 22 other species of turtles retrieved from NCBI,a crocodile and a lizard were used as outgroup,and the maximum likelihood method was used to analyze the combined sequence data of 13 mitochondrial protein coding genes GTR + G + I was selected as the best base substitution model to reconstruct the phylogenetic tree of turtles,so as to explore the phylogenetic status of ground turtles in turtles.The ML tree showed that batagur trivittata and pangshura sylhetensis first formed a sister group,then formed a branch with the ground turtles,and then formed a branch with the other six genera of the family.Based on the habitat distribution of turtles,the closest relationship between the two genera was determined.