SSR screening and characterization analysis based on full-length transcriptome sequencing of Potamocorbula ustulate
The paper is to comprehensively understand the distribution characteristics of SSR in the transcriptome of Potamocorbula ustulata,and to fully develop SSR molecular markers for practical use.P.ustulata,a kind of small type shellfish,is widely distributed in China's estuary areas.P.ustulata has a delicious taste and is rich in nutrients,so it is an excellent natural food for shrimp and crab,resulting in a significant reduction in resources.To better protect the resource of P.ustulata,it is necessary to understand its population genetic structure.P.ustulata with a shell length of(20.18±1.21)mm and a weight of(1.16±0.24)g were collected.In genetics,microsatellites have become important molecular markers for genetic diversity and marker-assisted breeding,because of their unique advantages,such as abundant polymorphism,codominance and conservation.Transcriptome sequencing technology can simplify and enhance the development of SSR markers.SMRT sequencing can generate longer reads based on second-generation sequencing,and it can be used to explore new genes and discover new SSR loci.In this study,Illumina RNA-Seq technology and SMRT sequencing technology were used for full-length transcriptome sequencing of P.ustulata.MISA software was used to screen SSR loci and analyze their compositional characteristics,providing important basic data for subsequent genetic research and marker-assisted breeding of P.ustulata.Based on transcriptome sequencing,38 964 Unigenes were obtained for P.ustulata.MISA software was used to analyze the distribution of simple sequence repeat(SSR)in its transcriptome,resulting in the detection of 4 746 SSR loci distributed among 3 962 Unigenes,and there were 144 types of SSR repeat motifs.The frequency of occurrence was 12.18％,with an occurence frequency of 10.17％,and on average,one SSR site appeared every 11.33 kb.In addition,593 Unigenes contained two or more SSR loci,and 473 Unigenes contained compound SSR loci.The SSR repeat nucleotide types in the transcriptome of P.ustulata were analyzed,and the results showed that the main repeat unit types of SSR for P.ustulata were mononucleotide,dinucleotides,and trinucleotides,which respectively accounted for 47.64％,13.7％and 23.56％of the total SSR.A/T and AT/TA were respectively the dominant repeat motifs for the single nucleotide and dinucleotide,indicating a preference for A/T in the distribution of SSR sites within P.ustulata transcriptome.Moreover,SSR sites were mainly repeated 5-10 times,accounting for 62.18％of the total number of sites,and the length of SSR sites mainly concentrated in 12-20 bp,accounting for 42.58％of the total number of SSRs,larger than 20 bp accounted for 11.53％,and SSR sites containing low-level repeating elements(dinucleotide and trinucleotide repeats)were mostly present.These results indicate that the SSR loci in P.ustulata transcriptome are rich in types and have high polymorphism potential.This study can provide a foundation for the development of P.ustulata SSR molecular markers,germplasm resource utilization,and genetic diversity evaluation.
万方数据
维普
