The Genetic Basis Of High-elevation Adaption And The Cold Tolerance Mechanism Of Triplophysa Bleekeri

Triplophysa bleekeri,a member of Triplophysa species,is mainly distributed in the stem streams and tributaries of the Jinsha,Yangtze,and Yellow River.Compared with the other Triplophysa species inhabited in Qinghai-Tibetan Plateau(QTP),T.bleekeri occurs at lower elevations(200?3,000m).Based on the results of the reproductive study,a scholar proposed a hypothesis that T.bleekeri has the ancestral characters related to high-elevation adaption(Zhijian Wang,2011).Therefore,it is worth discussing whether T.bleekeri has the genetic basis of high-elevation adaption.In this study,we sequenced the genome of T.bleekeri,and tried to search the answer from the perspective of genomics.Comparative genomic analyses were performed to investigate whether T.bleekeri has the high-elevation adaption as with T.tibetana(4,000?5,000m)and T.siluroides(3,000?4,000m)based on genomic data.The temperature of rivers and lakes on QTP is always low,and the fish of QTP evolved the cold acclimation.The temperature acclimation of fish is largely genetically determined.T.bleekeri has a special characteristic that it can spawn in the coldest seasons,which suggests that T.bleekeri has the genetic basis of cold acclimation.However,how the physiological functions and metabolic processes of T.bleekeri acclimate the cold temperature? To explore this question,we combined transcriptomics and lipidomics to investigate the cold tolerance mechanism of T.bleekeri.The details of research content and major results are as follows,(1)The genome sequencing of T.bleekeri.The genome of T.bleekeri was sequenced with the Pac Bio platform,and the chromosome assembly using Hi-C technology.Here,we assembled a chromosomal genome sequence of T.bleekeri,with a size of ?628 Mb(contig and scaffold N50 of 3.1 and 22.9 Mb,respectively).The genome sequences were anchored upon 25 chromosomes,highlighting a high chromosome anchoring rate of 96.2% on the base level.21,198 protein-coding genes were predicted in the T.bleekeri genome,and 97.3% of the protein-coding genes were functionally annotated.(2)The phylogenetic analysis and historical effective population size inference for T.bleekeri.The result showed that T.bleekeri is phylogenetically closer to T.tibetana and T.scleroptera.Divergence time estimation showed that T.bleekeri diverged from their common ancestor,T.scleroptera and T.xichangensis,?25.3 million years ago(Mya).PSMC analysis results showed that the effective population size of T.bleekeri reached a peak of about 0.6–0.7 Mya.However,the T.bleekeri population size experienced a dramatic decrease afterward.We speculate that the ancient T.bleekeri populations were affected by the accelerating QTP uplift and the quaternary glaciation.(3)The genetic basis of high-elevation adaption of T.bleekeri.The positively selected genes(PSGs)of T.bleekeri,T.tibetana,and T.siluroides were analyzed using PAML with the branch-site model.The GO and KEGG enrichment analyses were performed on PSGs,and the shared PSGs for the three Triplophysa species were identified.The results showed that the shared PSGs are involved in DNA repair pathways.It suggests that T.bleekeri has the genetic basis of high-elevation adaption as well as T.tibetana,and T.siluroides,and that some convergent genetic mechanisms were observed in these three species.(4)The cold tolerance of T.bleekeri.In this study,the cold stress experiment was conducted and transcriptomics and lipidomics were performed to investigate the cold tolerance mechanisms of T.bleekeri.The results showed that the differential expressed genes(DEGs)were involved in the lipid biosynthesis pathway and that the contents of polyunsaturated fatty acids and glycerophospholipid increased,suggesting that the lipid biosynthesis of T.bleekeri increased under low temperature.Besides,the gene expression of key enzymes of glycolysis increased which indicates that glycolysis was enhanced under low temperature.Besides,the DEGs are also involved in thyroid hormone synthesis and innate immune response pathways,indicating that these pathways are related to cold acclimation.Overall,we present a chromosomal-scale genome assembly of T.bleekeri.The adaptive evolution analyses were performed based on genomic data,and the results showed that T.bleekeri,T.tibetana,and T.siluroides have a similar genetic basis of adaption.Our study also investigated the cold tolerance mechanism of T.bleekeri,and the results showed that the lipid metabolism pathways play an important role in the cold resistance of T.bleekeri.