Cavefi sh can be important models for understanding the relationships among evolution,adaptation,and development in extreme environments.However,cavefi sh remain poorly studied,particularly at the genome level.Here,we...Cavefi sh can be important models for understanding the relationships among evolution,adaptation,and development in extreme environments.However,cavefi sh remain poorly studied,particularly at the genome level.Here,we sequenced the complete mitogenome of three cavefi sh in the family Nemacheilidae(Paranemachilus pingguoensis,Oreonectes polystigmus,and Heminoemacheilus longibarbatus),which were collected from karst caves in South China.The mitogenomes each contained 37 genes(13 protein coding,22 tRNA,and two rRNA genes)and a single control region,with the same genetic arrangement and distribution as those found in vertebrates.The non-synonymous/synonymous mutation ratios(Ka/Ks)of the mitogenomes indicated that the protein-coding genes(PCGs)of the three cavefi sh evolved under purifying selection.The mitogenomes of the three cavefi sh exhibit nucleotide composition biases for PCGs,tRNAs,rRNAs,and the whole genome,indicating that the mitochondrial DNA might have been subjected to evolutionary selection in response to extreme cave environments.Divergence time and evolutionary history analyses suggested that the speciation and diversifi cation of the cavefi sh coincided with the Miocene uplift of the southern Qinghai-Tibet Plateau,which greatly changed cave habitats.Overall,our study sheds light on the mitogenomes,phylogeny,and evolutionary history of nemacheilid cavefi sh.展开更多
基金Supported by the Open Fund of Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture(No.GXKEYLA2019-05)the National Natural Science Foundation of China(No.41806170)the China-ASEAN Maritime Cooperation Fund(No.CAMC-2018F)。
文摘Cavefi sh can be important models for understanding the relationships among evolution,adaptation,and development in extreme environments.However,cavefi sh remain poorly studied,particularly at the genome level.Here,we sequenced the complete mitogenome of three cavefi sh in the family Nemacheilidae(Paranemachilus pingguoensis,Oreonectes polystigmus,and Heminoemacheilus longibarbatus),which were collected from karst caves in South China.The mitogenomes each contained 37 genes(13 protein coding,22 tRNA,and two rRNA genes)and a single control region,with the same genetic arrangement and distribution as those found in vertebrates.The non-synonymous/synonymous mutation ratios(Ka/Ks)of the mitogenomes indicated that the protein-coding genes(PCGs)of the three cavefi sh evolved under purifying selection.The mitogenomes of the three cavefi sh exhibit nucleotide composition biases for PCGs,tRNAs,rRNAs,and the whole genome,indicating that the mitochondrial DNA might have been subjected to evolutionary selection in response to extreme cave environments.Divergence time and evolutionary history analyses suggested that the speciation and diversifi cation of the cavefi sh coincided with the Miocene uplift of the southern Qinghai-Tibet Plateau,which greatly changed cave habitats.Overall,our study sheds light on the mitogenomes,phylogeny,and evolutionary history of nemacheilid cavefi sh.
