Cytochrome c oxidase subunit Ⅰ gene-based genetic characteristics of Rattus tanezumi in domestic rodent plague foci of Yunnan Province
Objective To sequence and analyze the cytochrome c oxidase subunit Ⅰ(COⅠ)gene of Rattus tanezumi in the domestic rodent plague foci of Yunnan Province,China,and to explore the genetic characteristics of R.tanezumi populations in different geographical areas of Yunnan Province.Methods From 2016 to 2019,R.tanezumi was captured in Dali Bai Autonomous Prefecture(Dali),Baoshan,Dehong Dai and Jingpo Autonomous Prefecture(Dehong),Lincang,Yuxi,Wenshan Zhuang and Miao Autonomous Prefecture(Wenshan),and Xishuangbanna Dai Autonomous Prefecture(Xishuangbanna).A total of 408 liver and spleen specimens of R.tanezumi were collected to extract genomic DNA and then amplify the COⅠ gene by PCR.Bioinformatics methods were used for nucleotide and haplotype analysis of the COⅠ gene sequence.A molecular phylogenetic tree was constructed by using the neighbor-joining method.An analysis of molecular variance(AMOVA)among populations were performed,and gene flow and the genetic differentiation index(Fst)were caculated.Results The COⅠ gene sequences of 408 R.tanezumi specimens from the seven areas of Yunnan Province were successfully amplified.In the 639 bp COⅠ gene sequence,the average percentages of T,C,A,and G bases were 29.67％,25.67％,27.67％,and 16.99％,respectively,and the proportion of A+T was higher than that of C+G.A total of 23 haplotypes were identified in the seven geographical populations.The haplotype diversity was 0.433-0.846,and the nucleotide diversity was 0.002 82-0.019 73.The overall haplotype diversity of 7 populations from high to low was:Dehong>Yuxi>Baoshan>Wenshan>Xishuangbanna>Lincang>Dali.The Wenshan,Dehong,and Yuxi populations were more diverse by nucleotide.The molecular phylogenetic analysis showed that the haplotypes of the seven populations were divided into three clades.The haplotype network showed that the haplotypes were distributed in a mixed pattern across different geographical populations.The Fst showed significant differences between different geographical populations(all P<0.05),except between Baoshan and Xishuangbanna,Lincang,and Wenshan,between Xishuangbanna and Lincang and Wenshan,and between Lincang and Wenshan.Gene flow data revealed a certain degree of genetic differentiation between Yushan populations and Dali,Baoshan,and Xishuangbanna populations,while there was a lack of gene exchange among other populations.The AMOVA analysis showed that the genetic variation among the seven R.tanezumi populations mainly was intra-population variation,with a low level of inter-population variation.Conclusions The R.tanezumi populations of the seven cities or prefectures have high genetic diversity,and genetic differentiation is present between some geographical populations.This study provides a reference for the study of molecular ecology of R.tanezumi.
Rattus tanezumiCytochrome c oxidase subunit Ⅰ geneGenetic diversityGenetic differentiation
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