Evolution Of The Mitochondrial Genome Structure In Snake,with The Biogeography Analysis Of Protobothrops

The mitochondrial genome of snake include 13 protein-coding genes,2 rRNA genes,22 tRNA genes,one or two control regions.Comparing with the typical vertebrate mitochondrial genome,snake has its own unique structure.Duplication of control regions are usually found in other taxa,and most duplicated control regions are evolved concertedly.Duplication of control regions and concerted evolution have maintained 7,000 years in snake mitochondrial genomes.Protobothrops contains 14 species,mainly distributed in Qinling Mountains and Huaihe,South Asia,the Central South Peninsula and the Ryukyu Islands.In this study,we sequenced nine snake complete mitochondrial genomes by Sanger sequencing technology,and relevant snake mitogenomes were downloaded from GenBank.Besides,we also sequenced the mitochondrial and nuclear gene.Combined on the sequence determined in this study and related sequences in the NCBI database,we explored the following three issues:(1)structural patterns,organization and evolutionary implications,and possible rearrangement mechanism in the snake mitochondrial genomes;(2)the evolution pattern of control regions in Alethinophidian species;(3)the origin and dispersal path of Protobothrops.The main results of this paper are as follows:(1)The snake mitochondrial genome structure evolutionExamining 94 complete mitochondrial genomes from Serpentes,the result showed that among them,twelve types of mitochondrial gene arrangement patterns in total(Type ?,?,?,?-A,?-B,?-B1,?-B2,?-C,?-D,?-E,?-F,?-G)were detected.Type ?,? and? originated from an unknown or uncertain ancestor mitochondrial genome arrangement.The other nine types were directly or indirectly originated from type ?,each of them has their own unique characteristics.In snake mitogenomes,the rearrangements mainly involved four processes,gene loss,translocation,insert and duplication.Within Scolecophidia,the OL was lost twice independently,but persisted as a plesiomorphy in theAlethinophidia.Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes.Independently and stochastically,the duplication of pseudo-Pro(P*)emerged in seven different lineages,indicating that the presence of P*was a polytopic event in the mitogenome.The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots of mitogenome rearrangement.The maintenance of duplicate control regions and Asymmetry may be the source of its structural diversity.(2)The evolutionary pattern of duplicated control regions in snake genomesIn order to analyzed the evolutionary pattern of control regions,the control regions of 88 Alethinophidian species were downloaded from GenBank.Naja atra was selected as representative group to explore the more accurate evolution pattern of the duplicated control regions using RDP4 software to detect and analyze the multiple recombination sites.The results of the study showed that paralogous control regions(CR1 and CR2)from the same species were clustered together,and orthologous control regions(CR1 or CR2)from different species were separated from each other.However,in a small part of the mitochondrial genome of snakes,the results were different:their orthologous control regions were clustered together,and paralogous control regions were separated from each other.In Alethinophidia species,the duplicated control region owned evolution pattern:concerted evolution and independent evolution.Concerted evolution was widely found in most groups,while independent evolution only occured in a few groups,rather than a single and accidental phenomenon.The result indicated the duplicated control regions of N.atra were originated from the heterologous recombination and evolved independently.All functional areas exist in the individual control regoins,without degradation.It is presumed that recombination may maintain a high degree of similarity in the process of long-term independent evolution.(3)Biogeography of protobothropsFour mitochondrial and six nuclear genes were selected to construct the phylogenetic relationships of Protobothrops.Combined with the evidence of divergence time,palaeoclimate and palaeogeography,we studied the biogeography of this genus,and deduced its origin center and dispersal route of the subgroups.The results show that protobothrops was originated from the early Miocene(20.64 Ma),the divergence occured in 17.20 Ma,fourteen species were divided into four clades.The ancestral distribution of Protobothrops existing species was located in southwestern China and adjacent areas,preaded to the Qinghai-Tibet Plateau,and central and eastern China,respectively.It has experienced 38 dispersal events and 11 vicariant events,and formed the modern distribution pattern.