| With the commercialization of whole-genome sequencing,the cost of sequencing is reduced,the application is becoming more and more extensive and in-depth.Especially in biological diversity,population history dynamics,adaptive evolution and other aspects have important applications.The study on population evolution process of the tiger and the formation mechanism of species diversity,can not only deepen the understanding of the tiger,also provide reference for other species research combines the genomics with population genetics.The most important thing is to restore the population genetic diversity and finally release animals to nature.The tiger(Panthera Tigris)is the largest cat.In the ecosystem,tiger is at the top of the food chain and has the function of regulating ecological balance and species diversity.The tiger subspecies under different geographical conditions have undergone great changes in some aspects of the body.The physiology difference such as the fat,food digest and metabolism,appearance difference such as color,coat pattern,body size and so on.The study of formation mechanism is better to understand the species differences caused by regional differences,as well as the evolution for adapting to the environment.Meanwhile providing reference for the evolution mechanism of other subspecies and organisms.For the protection of endangered wild animals,to understand the history of their living condition and the relationship between population change and environmental laws,which play an important role for the corresponding protection measures.In this paper,the whole genome of 5 amur tigers and 3 South China tigers was resequenced by using next generation sequencing.To study the genetic structure and gene exchange of each group base on SNP and CNV,we get the fellowing conclusions:1.Through whole genome resequencing,we obtain 647 Gb high quality clean datas,the average sequencing depth is 27.5x.A total of 6.3 million high-quality SNPs was obtained,with 4.29 million(67.9%)SNP in the non-coding region,and 18534 non-synonymous SNPs and 25,148 synonym SNPs in the coding region.A total of 1.73 million InDels were obtained,of which 860 thousand(49.8%)were insertion and 870 thousand(50.2%)were deletion,and the InDels in the coding region had 2114(0.12%).A total of 270 thousand CNVs were obtained,of which 260 thousand(97.5%)were deletion,and 6783(2.5%)were duplication.On average,each individual contains 32676 CNV,with an average length of 4029bp.2.The phylogenetic tree of two tiger subspecies was constructed by Neighbor-Joining method.From the evolutionary tree we can see that the two subpopulations obvious differentiation.The genetic distance and variation degree between the subspecies were analyzed base on the mitochondrial genome,the smallest genetic distance amoung subspecies were the amur tiger and bengal tiger,and the biggest was bengal tiger with sumatran tiger and southern China tiger.But the genetic distance between southern China tiger and sumatran tiger was small.Through rebuilding tiger and several common mammalian mitochondrial phylogenetic tree,we estimated the divergence time amoung 9 mammalian genomes.About a million years ago the tiger was separated from other eight mammals.And more than a million years ago,the tiger has lived together with our ancestors.3.The PC A analysis of amur tiger and South China tiger showed significant differences between them at the whole genome level.The results showed that the difference between amur tiger and South China tiger was significant,which was consistent with the results of the evolutionary tree and PCA analysis.PSMC analysis 8 tiger population history dynamic learns that eight tiger subspecies have a common ancestor,and in about 700 thousand years ago,populations have an expansion,and has achieved the highest population(Ne=30 thousand).4.From selective sweep analysis based on SNP,we screened 133 and 182 sweep regions in amur tiger and South C hina tiger,respectively.Getting rid of 79 common regions,we get 45 and 103 regions in amur tiger and South China tiger,respectively.In amur tiger and South China tiger,there has similar GO enrichment and KEGG pathway analysis,both of the genes mainly enrich in 9 kinds of biological functions,which involved in 22 genes in energy metabolism,9 genes involved in muscle contraction function and 20 genes related to carnivorous feeding.In KEGG pathway analysis,there are 200 and 192 biochemical pathways in amur tiger and South China tiger,respectively.In these pathways analysis we found 38 genes involved in disease pathways and that may associate with tiger susceptible disease and parasitic infections.5.Selective sweep analysis based on CNV,we identified 782 selected regions,the total length of these regions was 3.9Mb,and the average length was about 4.9Kb,including 94 genes.In addition to the results of SNP analysis,30 genes involved in olfactory function were found.6.In selected region,a total of 702 genes were found in amur tiger and 414 genes in South China tiger,both have 50 genes in common.It was found that the PRKG1 have strong positive selection signal and respond in cold adaptation in amur.TLE3 gene in amur tiger had a SNP non-synonymous mutation at P101L site,suggesting that the mutation of the P101L site may be the cause of the difference between the body size of amur tiger and South China tiger. |
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