Genetic Characteristics And Adaptive Evolution Of Acanthopagrus Latus And Rhabdosargus Sarba

Acanthopagrus latus and Rhabdosargus sarba belong to Actinopterygii,Perciformes and Sparidae.A.latus belongs to the genus Acanthopagrus and the R.sarba belongs to the genus Rhabdosargus.Both A.latus and R.sarba are fishes living in tropical and subtropical inshore waters,and generally migrate in a small area,mainly distributed in the East China Sea,South China Sea,southern Japan waters,Philippine waters and Indian waters.Due to the influence of natural environment and anthropogenic factors,A.latus and R.sarba resources have been declining to different degrees,and there are few studies on the genomics of both.With the continuous improvement of sequencing technology,population genomics,which combines population genetics and genomics,has emerged,and it can obtain the genetic characteristics of species populations and reveal the mechanisms of environmental adaptations.In this study,the mitochondrial control region sequences of A.latus were amplified,and the diversity and genetic differences among different geographical groups of A.latus were analyzed;a database of genomic variation in A.latus populations was constructed using the whole genome of A.latus available on NCBI as a reference by whole-genome resequencing technology,the evolutionary relationships,population structure and historical dynamics of A.latus based on the detected SNPs were analyzed,and candidate genes related to environmental stress in A.latus were screened to reveal the environmental adaptive evolutionary mechanism.The genetic variation,genetic structure and historical dynamics of A.latus population were analyzed to reveal the genetic characteristics of A.latus and the molecular mechanism of its adaptive evolution,and to provide a theoretical basis for the conservation of germplasm resources of A.latus.The study will elucidate the population genetic variation,genetic structure and population history dynamics of A.latus,reveal the evolutionary process and molecular mechanisms of adaptation to the environment of A.latus,and provide scientific basis for the conservation of germplasm resources of A.latus in China.Based on whole-genome resequencing technology,the genetic characteristics and adaptive evolution of A.latus and R.sarba in Wuyu were studied,the genetic variation information of A.latus and R.sarba were examined,a database of genomic variation was established,the genetic diversity of the two Sparidae species using genomic data was studied,and the mechanism of adaptive evolution of the two Sparidae species was explored.The main research contents and results are as follows:1.Genetic diversity analysis of A.latus population based on mitochondrial control regionA molecular phylogeographic study was conducted using mitochondrial control region(CR)sequences on a total of 109 wild A.latus individuals from six geographic populations collected in August or September 2022 in coastal China(Xiamen,Quanzhou,Wuyu,Dongshan,Zhanjiang and Beihai),and the results showed that all A.latus populations showed high genetic diversity,which was mainly related to their reproductive habits and growth rate,and could ensure a large number of supplementary populations.This is mainly related to its reproductive habit and growth rate,which can ensure a large number of complementary populations.In addition,both the neutrality test and nucleotide mismatch distribution analysis indicated significant deviations from neutrality among A.latus populations,suggesting that they have experienced population expansion events.This result may be that the Pleistocene ice age or accretionary release influenced the formation of the modern genealogical pattern of A.latus.2.Genetic characteristics and adaptive evolution of A.latus populations based on whole-genome resequencingThe whole-genome resequencing of 10 A.latus from each of the six geographical populations was conducted to analyze the molecular mechanisms of genetic structure and adaptive evolution of A.latus populations under different environmental stresses and identify related genes through bioinformatics analysis by high-throughput sequencing technology.From the resequencing of 60 samples,a total of 522.97 Gb were generated,with an average data volume of 8.72 Gb each sample and an average sequencing depth of 12.59 X.A total of 19,488,059 single nucleotide polymorphism(SNP)variants were obtained through sequencing data matching and genetic variation detection,and the distribution types of these loci mainly included intronic,intergenic,5’UTR,3’UTR,synonymous and nonsynonymous.The genetic diversity of A.latus populations did not differ significantly,and there was no genetic differentiation between different geographical groups of A.latus,and the level of differentiation within populations was greater than that between populations.Using Xiamen A.latus as the reference population,it was found that the selected genes NFIC,RAC2,NLR,AHIl,TATDN1,CCDC125,SCCPDH,LRRC40,BLVRA,PCDH,ARHGEF11 and JPH1 in Beihai,Dongshan,Quanzhou,Wuyu and Zhanjiang A.latus may form adaptive evolution related to growth and development,feeding,immunity and locomotion in the sea areas with high fishing pressure.Specifically,the adaptive evolution in tooth and bone development,scale formation,immunity,eye development,regulation of signal transduction,cell growth and locomotion of A.latus to adapt to a higher fishing pressure environment.3.Genetic characteristics and adaptive evolution of two Sparidae populations based on whole-genome resequencingThe whole-genome resequencing of 10 A.latus and 10 R.sarba from Wuyu was conducted by high-throughput sequencing technology.Through bioinformatics analysis,the molecular mechanisms of genetic structure and adaptive evolution of the R.sarba and A.latus population were analyzed and related genes were identified.The results showed that a total of 88.13 Gb were sequenced from 10 A.latus samples,with an average data volume of 8.81 Gb per sample and an average sequencing depth of 12.72 X.A total of 85.55 Gb were sequenced from 10 R.sarba samples,with an average data volume of 8.56 Gb per sample and an average sequencing depth of 12.36 X.A total of 42,441,316 SNP variants were identified in this study by comparison with the reference genome.441,316 SNP variants were identified.The results of principal component analysis and genetic diversity were calculated based on high quality SNPs.The results showed that the nucleotide polymorphism of A.latus was higher than that of R.sarba.The study screened the selected genes in A.latus and R.sarba in Wuyu Island,and the study on the adaptive evolution of A.latus and R.sarba in the same habitat revealed that:R.sarba may have developed adaptive evolution related to immunity,feeding,growth and development,and locomotion;A.latus may have developed adaptive evolution related to immunity,nervous system,growth and development and metabolism.