The High-altitude Adaptation Mechanism Of Vulpes In The Qinghai-Tibet Plateau

Due to the impact of the altitude,the Qinghai-Tibet Plateau(QTP)has a harsh living environment.Low oxygen levels,extreme temperatures,and high UV-radiation pose challenges to the survival of native species.Vulpes ferrilata and Vulpes vulpes montana are both distributed in the QTP and play important roles in maintaining the fragile ecosystem balance of the plateau.By exploring the high-altitude adaptation mechanism of the two species,we can not only expand our understanding of the high-altitude adaptation mechanism of species under different phylogenetic relationships,but also lay a solid molecular foundation for the subsequent development of scientific and effective protection and management measures for these two species of Vulpes.The results of this study are as follows:1.Through Next-Generation sequencing,Nanopore sequencing,and Hi-C sequencing,high-quality genomes of V.ferrilata and V.v.montana were obtained.The size of genome and Contig N50 of V.ferrilata were 2.37 Gb and 61.59 Mb,respectively.The size of the genome and Contig N50 of V.v.montana were 2.34 Gb and 47.68 Mb,respectively.In the Hi-C assisted assembly,157 Contigs were anchored to 18 chromosomes of V.ferrilata,with a mounting rate of 98.36 %.A total of 137 Contigs were attached to 17 chromosomes of V.v.montana,with a mounting rate of 99.51 %.The BUSCOs of the assembled genome were 92.76 % and 95.4 %,and the BUSCOs of the annotated genome were 94.98 % and 93.7 %,respectively.The qualities of the genome of the two species were better than those of other existing genome of Vulpes,filling the gap in the genome resources of the two species.2.The phylogenetic relationships based on comparative genomics showed that the phylogenetic relationships of the four species of Vulpes were consistent with previous studies based on trasncriptomic and mitochondria.In this study,the divergence time of V.ferrilata and V.corsac was 3.45-3.09 million years ago.The ancestors of the V.ferrilata and V.corsac diverged from the V.v.montana between 5.05 and 4.49 million years ago.The ancestors of V.lagopus and the other three Vulpes diverged between 6.05 and 5.38 million years ago.In addition,the divergence time of V.ferrilata and V.corsac obtained in this study was consistent with the time of the dramatic uplift of the QTP,which provides a more accurate reference for the divergence time of Vulpes and canids in a larger range.3.The analysis of gene family expansion and contraction based on comparative genomics indicated that low temperature and low oxygen content environment in QTP were important factors for the significant changes of gene families of V.ferrilata and V.v.montana compared with their low-altitude relatives.The GO terms enriched by the expanded gene families were mainly related to hypoxia and low temperature adaptation,while the GO terms enriched by the contracted gene families was mainly related to hypoxia adaptation.The results of KEGG enrichment showed that the KEGG pathways co-enriched by the expanded gene families of two Vulpes were also related to low temperature adaptation.4.The enrichment results of positive selection gene set based on comparative genomics showed that the enrichment results of positive selection gene set were mainly related to DNA damage repair,angiogenesis,and lipid metabolism,indicating that Vulpes had the same adaptation mechanism in the face of UV-radiation,low oxygen,and extreme temperature at high-altitude.The enrichment results of different gene sets obtained when the two species were foreground branches respectively indicated that the V.ferrilata and V.v.montana not only had the same adaptation mechanism to the high-altitude environment,but also had unique adaptation mechanism.Through database comparison and literature review,99 positive selection genes of the two foreground branches may be related to the adaptation of the V.ferrilata and V.v.montana to the low oxygen,high ultraviolet radiation,and low temperature of the QTP.5.The results of amino acid site substitution analysis of the two species showed that a total of 26 genes had parallel amino acid site substitution between the two species,which were mainly related to oxygen content,indicating that the low oxygen environment in the QTP was the main factor leading to parallel amino acid site substitution between V.ferrilata and V.v.montana.Further analysis of protein three-dimensional structure showed that the protein structure of four genes,STAB2 associated with hyaluronic acid binding and KLK13,DDX60 and IGSF22 associated with immunity,had significant changes,suggesting that their function had changed,which may be related to their high-altitude adaptation.6.The study based on comparative transcriptomics showed that the significantly high expression genes of the two species of high-altitude Vulpes were mainly reflected in hypoxia response,DNA damage repair,myocardial development and angiogenesis,suggesting that low oxygen content and high UV-radiation were the main factors causing the high expression of genes in Vulpes.The gene expression levels of three tissues of four Vulpes showed that the organs of Vulpes had a tissue-specific expression patterns on the whole,that is,the expression patterns of the same tissues of different species were more similar,regardless of altitude influence.In addition,altitudinal changes in gene expression patterns were also found in Vulpes,suggesting that Vulpes shared the same gene expression and regulation mechanisms in response to high-altitude selection pressures.In conclusion,this study conducted genome assembly and annotation at the chromosome level for V.ferrilata and V.v.montana distributed in the QTP,and explored the high-altitude adaptation mechanism of the two species by comparative genomics and comparative transcriptomics.The results showed that the two Vulpes had both the same and different high-altitude adaptation mechanisms.This study provides a new perspective for exploring the adaptation mechanism of species to high-altitude,and also lays a solid molecular foundation for further understanding of the adaptation mechanism of these two Vulpes.