SSR distribution and sequence characteristics analysis of Diptychus maculates based on high-throughput transcriptome sequencing

【Objective】This paper analyzed the SSR distribution and sequence characteristics of Diptychus maculates based on high-throughput transcriptome sequencing,to provide theoretical data for the development of SSR molecular markers,genetic diversity,genetic linkage map,germplasm resource identification and molecular assisted breeding of D. maculates.【Method】Illumina NovaSeq high-throughput sequencing platform was used to perform transcriptome sequencing on the skin tissue of D. maculates. Trinity was used to sequence and assemble the obtained high-quality sequencing data. MISA was used to analyze the SSR distribution and sequence characteristics of the screened Unigenes more than 1 kb.【Result】A total of 244.42 Gb of Clean data were obtained from the transcriptome of D. maculates. 55182 Unigenes were obtained after assembly,among which 8903 Unigenes contained SSR loci,and the proportion of Unigenes containing SSR was 16.13%,containing 12899 SSR loci. After 616 complex SSR loci were removed,a total of 12283 perfect SSR loci were obtained. There were 6 repeat motif types of mononucleotide-hexanucleotide,among which the number of mononucleotide repeat motif was the largest(6654,accounting for 54.17%). The number of dinucleotide-hexanucleotide decreased with the increase of nucleotide repeat number. They accounted for 32.30%, 12.04%, 1.38%, 0.07% and 0.03% respectively. There were a total of 348 different repeat motifs in the transcriptome of the D. maculates,of which 145 were trinucleotide repeat motifs(the most abundant and most varied). The mononucleotide was the type with the largest number of repeat motifs,and the type with the largest number of repeat motifs was the(A) ₁₀ type of mononucleotide. The length range of SSR was large,ranging from 10 to 75 bp,with a total length of 157088 bp. The relative abundance of SSR was 0.19%. The number of SSR with a length of 10 bp was the largest of a total of 3232,accounting for 26.31%. Followed by SSR with a length of 12,11 and 14 bp,accounting for 21.73%,12.02% and 10.06%,respectively.【Conclusion】In the transcriptome of D. maculates,the number of SSR loci is large,its occurrence frequency is high,and the polymorphism is good,which can be used to develop molecular markers of D. maculates. And the number of different nucleotide repeat motif types is greatly varied,and the distribution characteristics are obviously different.