| Charybdis japonica is widely distributed in coastal waters such as the East China Sea,the Bohai Sea,and the Yellow Sea in China.Habitat environment is the basis of species survival,and the adaptability of the same widely distributed group to the corresponding habitat is inconsistent.Temperature is one of the indispensable environmental conditions for marine species,and the adaptive mechanisms of widely distributed species populations in response to the environmental temperature changes in their habitats are also different.At present,the adverse effects of global climate change on the marine environment have brought damage to the abundance and distribution of C.japonica.resources.Therefore,it is particularly important to describe the adaptability of different geographical groups of C.japonica.to the habitat environment.In this study,transcriptomics were selected to analyze the five geographic populations of C.japonica.,which laid the foundation for elucidating the genetic diversity of different geographic populations of C.japonica.at the molecular level.Mainly including the following aspects:1.Comparative transcriptome study of different geographical populations of C.japonica.C.japonica is widely distributed,and the habitat environment is the basis for the survival of the species.Therefore,in order to explore whether there are differences in the adaptability of C.japonica populations to their habitats,comparative transcriptome analysis was performed on five populations of C.japonica.A total of 185.19Gb clean reads were obtained from 24 samples from 5 populations,and the proportion of sequences with base mass greater than Q30 was at least 89.92%.The genomic data of clean reads and C.japonica were compared,and the results showed that the total matching degree of the five populations of C.japonica was 60.43%-88.38%,indicating that the reliability of transcriptome sequencing results was high.The results showed that a total of 46,231 new transcripts were obtained,including 3,227 new genes.In addition,compared with the Zhoushan control,the Lianyungang,Yantai,Dalian and Taizhou populations had 1,362,646,238 and 211 highly expressed genes and 2,188,770,181 and 113 low expressed genes,respectively.The GO enrichment results by differentially expressed genes indicated that their differential genes were mainly enriched in GO terms of translation,protein kinase activity,ribosome,and GTPase activity.From the KEGG enrichment results,most of the KEGG enrichment pathways in the five populations were related to signal transduction,translation,transport and catabolism,and cardiovascular diseases.There was no significant enriched pathway in the group of Zhoushan population vs Yantai population,while the most significant expression was found in the group of Zhoushan population vs Lianyungang population.Since there was no significant enrichment pathway in the Zhoushan group vs.the Yantai group,it is speculated that the adaptive differences were not significant due to the close geographical location and the similar environmental temperature and salinity of the habitats.Combined with the annotation information of differentially expressed genes,it can be hypothesized that these pathways are related to metabolism,growth,and immunity,suggesting that all five populations of the C.japonica differ in their mechanisms of adaptation to the environment.2.Comparison of transcriptome among different geographical populations of C.japonica under temperature stressC.japonica is a crustacean.As a temperature-changing animal,the environmental temperature is one of the most important living conditions for crustaceans.In this study.the transcriptome of southern(Zhoushan)and northern(Dalian)populations of C.japonica under high and low temperature stress was studied.The results showed that 107.26Gb clean reads were obtained from the original data of 18 samples after filtering,and the proportion of sequences with base mass greater than Q30 was at least 89.42%.The results showed that the total matching degree was 74.80%-89.16%.In addition,there are 45,952 new transcripts,including 3,124 new genes.In addition,there were 45,952 new transcripts,including 3,124 new genes.In the Zhoushan population,there were 28 and 5 down-regulated genes in the Zhoushan high-temperature group compared with the Zhoushan control group;68 up-regulated genes,and 870 down-regulated genes in the Zhoushan low-temperature group.In the Dalian population,compared with the Dalian control group,the Dalian high-temperature group had 84 up-regulated genes and 196 down-regulated genes;the Dalian low-temperature group had 182 up-regulated genes and 127 down-regulated genes.Under high and low-temperature stress,the most significant GO terms of differentially expressed genes in Dalian and Zhoushan populations were related to physiological processes such as protein synthesis,cell division,signal transduction,cell growth,development,and senescence.enrichment of KEGG pathways showed that differentially expressed genes in high and low-temperature groups of the Dalian population were enriched in 152 and 100 pathways,respectively,while differentially expressed genes in high and low-temperature groups of the Zhoushan population were enriched in 152 and 100 pathways,respectively.The differentially expressed genes in the high-temperature and low-temperature groups of the Zhoushan group were enriched in 7 and 88 pathways,respectively.Combined with the annotation information of differentially expressed genes,it was hypothesized that the differentially expressed genes in the two C.japonica populations under temperature stress were mainly related to signal transduction,lipid metabolism,immune system,and immune diseases.3.Study on genetic structure of C.japonica population based on SNP locus of transcriptomeIn order to understand the population genetic diversity of C.japonica,the genetic structure of the C.japonica population was analyzed based on SNP results of transcriptome data.The results showed that there were 612,604 SNP loci detected in five geographical groups,the main variant SNP loci were base conversion,and the ratio of transformation to transversion(Ti/Tv)was 2.30.The results also showed that 91,726 SNP variants were detected,most of which were located in the intergenic region,followed by exon region and UTR3.There are 22,583 SNPs located in the gene’s coding region,among which synonymous and non-synonymous mutations account for 99.76%.According to the phylogenetic tree,the five populations are divided into two populations,and there are differences between the south(Zhoushan and Taizhou populations)and the north(Dalian,Lianyungang and Yantai populations),and the genetic differentiation between Zhoushan population and Dalian population is the most obvious.The results of GO enrichment showed that the most significant of the five populations were nuclear,endoplasmic reticulum membrane,membrane and microtubule-dependent movement.KEGG enrichment results showed that the candidate genes of five populations of C.japonica were mostly enriched in selenium metabolism,hippo signaling pathway-flying,cytotoxicity mediated by natural killer cells,platelet activation,ABC transport and other pathways,which indicated that there were differences in immune,cell proliferation and apoptosis-related pathways among five geographical populations of C.japonica.The results showed that the genetic diversity of C.japonica germplasm was rich and had obvious regional distribution law.In this study,firstly,the transcriptome analysis of five populations of C.japonica was carried out,and it was found that the adaptability of northern and southern populations to the environment was different.Then,some key pathways and genes related to temperature were found through the transcriptome analysis of the southern(Zhoushan)population and the northern(Dalian)population.Finally,based on the phylogenetic tree analysis,population principal component analysis and candidate gene enrichment path analysis of SNP loci in transcriptome data,it was found that there was an obvious geographical distribution law among populations of C.japonica. |
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