Genome Survey Analysis And SSR Locus Mining Of Three Marine Fishes

Argyrosomus japonicus,Doederleinia berycoides and Hapalogenys analis all belong to the order Perciformes.The three marine fishes are important economic species in China,with high edible value and ecological value.In recent years,due to the impact of overfishing,human activities,and environmental changes,its resources have declined sharply,and there is an urgent need to carry out research on artificial aquaculture.In order to better carry out aquaculture research on three marine fish species,it is particularly important to explore their germplasm resources,as well as the genetic diversity and genetic structure of populations.Microsatellite molecular markers have great advantages in studying species germplasm and genetic information.In this study,the genomic survey sequencing was used to develop microsatellite loci for three marine fish species.The main research results are as follows:1.A total of 84.27 Gb of sequencing data was obtained from A.japonicus through genome survey analysis.The genome survey sequencing results showed that the genome size of A.japonicus was about 675 Mb,and its heterozygosity ratio and repeated sequences were 0.21%and 35.47%.respectively.Microsatellite loci were detected from the genome survey data of A.japonicus,and 316.357 perfect microsatellite loci were obtained.Dinucleotide repeats were the most abundant microsatellite types,accounting for 43.06%,while hexanucleotide repeats were the least,accounting for 0.10%.In the repeated unit,the amount of A/T is the largest,accounting for 38.72%and the number of repeated units containing GC is low.The number of microsatellite loci with 10 and 6 repeats was the highest.2.A total of 85.62 Gb of sequencing data was obtained from the genome survey analysis of the D.berycoides.The results of genome survey sequencing showed that the genome size of the D.berycoides was about 696 Mb,and its heterozygosity ratio and repeated sequences were 0.37%and 31.62%,respectively.A total of 462,395 perfect microsatellite loci were detected based on the genome survey data of heterozygosity ratio and repeated sequences.The number of dinucleotide repeats is the largest,accounting for 58.49%,while hexanucleotide repeats accounted for the least,only 0.13%.In the repeat unit,A/T is the dominant repeat unit,accounting for 24.95%,and the number of repeated units containing GC is low.The number of microsatellite loci with 10 and 6 repeats was the highest.3.A total of 83.02 Gb of sequencing data was obtained from the genome survey analysis of H.analis.The genome survey sequencing results showed that the genome size of H.analis was about 543 Mb,and its heterozygosity ratio and repeated sequences were 0.45%and 26.78%,respectively.A total of 280,378 perfect microsatellite loci were detected in the survey data of H.analis.The proportion of dinucleotide repeats is as high as 56.05%,while the proportion of hexanucleotide repeats is only 0.45%.Among the repeat units,A/T is the dominant repeat unit,accounting for 22.37%,and the number of repeated units containing GC is low;The number of microsatellite loci with 10 and 6 repeats was the highest.4.Population genetic testing of a test population using 20 polymorphic microsatellite loci selected from the survey sequencing results of H.analis.The results showed that the number of alleles(Na)at each point ranged from 5 to 13,with a mean of 8.75.The average observed Ho and He were 0.808 and 0.863,respectively.The PIC was 0.826,and both were higher than 0.5.After Bonferroni correction,5 loci significantly deviated from the Hardy Weinberg equilibrium(P<0.001).There are 4 loci with invalid alleles.The developed microsatellite loci can be used for future genetic breeding and population genetics research of H.analis.Using 8 microsatellite loci to analyze the genetic structure of 3 populations of H.analis.The results showed that the allele abundance(AR),Ho,He,and PIC of the three populations of H.analis were higher,showing a high level of genetic diversity.Fst value showed that there was significant genetic differentiation between the cultured population in 2022 and the cultured population in 2020,while the wild population in 2021 had smaller genetic differentiation from the other two populations.The analysis results obtained by UPGMA tree and 3D-FCA are consistent with those obtained by Fst value analysis.