| Charybdis japonica is an important seafood edible crab in China,with high economic value and nutritional value.As a result of climate warming,the marine environment is undergoing significant changes,especially with rising temperatures affecting the spatial distribution and diversity of marine life,especially coastal species.Improving our understanding of temperature adaptation is essential for predicting the adaptive capacity and ecological consequences of global warming.In this study,whole genome resequencing technology was used to elucidate the genetic structure of C.japonica at the whole genome level,and to understand how Japanese toad populations at different latitudes adapt to different geographical environments.The results that follow are the primary study findings:(1)Genetic structure of C.japonica population elucidated based on whole-genome resequencing.In this study,a map of genetic variation in C.japonica was drawn and a large amount of genetic variation information was obtained.Whole-genome resequencing was performed on 19 samples from 4 C.japonica populations using technique called wholegenome resequencing,with a total of 2796.68 Mb clean reads.The high-quality clean reads were located to the reference genome of C.japonica,with an average alignment rate of 94.36%,a pairwise average alignment rate of 93.96%,an effective average alignment rate of 87.62%,an average coverage depth of more than 13.52 × per individual,and an average genome coverage(1×)of 79.50%.By detecting the genetic variation information of single nucleotide polymorphisms(SNPs)and insertion/deletion(InDels)in the C.japonica population,10,210,179 SNPs were distributed on 51 chromosomes,mostly concentrated at the end of chromosomes,and the number of distributions was positively correlated with the length of chromosomes.Most of the variants were located in intergenic regions,a total of 7,320,190,accounting for 71.70%of the total number of SNPs,followed by 2,295,322 SNPs in the intronic region(22.48%).The number of SNPs causing synonymous mutations was up to 99,979(52.14%),and the number of SNPs causing nonsynonymous mutations was 88,351(46.08%).The types of base mutations were mainly C->T and G->A,followed by A->G and T->C.Each sample’s transition/transversion(Ts/Tv)number is greater than 1.89.A total of 2,112,157 InDels were detected on 51 chromosomes,mostly concentrated at the end of chromosomes,and the number of distributions was positively correlated with the length of chromosomes.Among them,there were 892,793 inserts and 1,151,460 deletion,and the percentage of Indel distribution showed a downward trend with the increase of its length,and the length of the vast majority of Indels was lbp(44.69%)and 2bp(20.50%);The largest number of Indels was located in the intergenic region,with a total of 1,511,961;followed by the number of Indels in the intronic region with 3,751,711,being responsible for 32.916%of all Indels;The maximum number of Indels resulting in frameshift mutations was 13,008(72.38%),including 6,030 insertion variants(33.55%)and deletion mutations 6,978(38.82%);The number of InDels resulting in nonframeshift mutations was 4,475(24.90%),including 1,541 insertion variants(8.57%)and deletion variants 2,934(16.32%).Based on the high-quality SNP dataset of four Japanese crab populations,phylogenetic tree construction,PCA principal component analysis and population structure analysis showed that the four groups were differentiated into two groups,namely the northern group(Dalian group and Lianyungang group)and the southern group(Zhoushan group and Taizhou group).The effective population size of the C.japonica has been declining since the glacial age and is still at a low level.(2)Detection of selective signals based on whole-genome resequencing and candidate genes’ enrichment.To identify candidate genes linked to temperature adaptation in different geographic populations.In this study,we used the high-quality SNP dataset obtained to detect and analyze the distribution of genome-wide selection signals of four C.japonica populations based on the fixation index(Fst).The top 5%of the Fst value was selected as the selection threshold,and the sites within the threshold were defined as strong selection signal sites,and the genes located within the threshold were selected as candidate genes.A total of 162 candidate genes were screened by Fst selective clearance method.The candidate genes were enriched to understand its function,GO annotation and functional enrichment analysis found that the candidate gene was mainly annotated in molecular function(MF),followed by biological process(BP),mainly enriched in acetyl-CoA carboxylase activity(GO:0003989)lipid metabolism process(GO:0006629),lipid biosynthetic process(GO:0008610),calcium ion transmembrane transport(GO:0070588)and other GO terms related to enzyme activity,substance metabolism,biosynthesis process and material transport.KEGG pathway enrichment analysis found that the enrichment results of these candidate genes mainly focused on fatty acid biosynthesis(ko00061),glycerophospholipid metabolism(ko00564),drug metabolism-cytochrome P450(ko00982),Insulin signaling pathway(ko04910)and glycolysis/gluconeogenesis(ko00010)and other pathways such as lipid metabolism,glucose metabolism,immunity and oxidative stress.Some genes related to temperature adaptation were involved in the regulation of lipid metabolism,energy metabolism,molting,immunomodulation,oxidative stress,DNA damage repair and apoptosis,and the expression of genes regulating immunomodulation(ARHGAP45),DNA damage repair(CXXC1)and energy metabolism(GlyP)was higher in the four populations.In this study,the results of genome-wide resequencing analysis of four C.japonica populations showed that the four groups were divided into two populations,and by comparing the geographical differences and localization chromosomal differences of temperature-selective genes in different latitude groups in Dalian,Lianyungang,Zhoushan and Taizhou,and enrichment analysis,the selected genes were adapted to different temperatures by regulating physiological processes such as energy metabolism,lipid metabolism,immune regulation,and oxidative stress.This has promoted research on crab genetics and conservation breeding in China;more accurate prediction of the adaptive potential of fishery organisms to environmental stresses. |
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