Identification and characteristics analysis of SSR loci in the transcriptome of Tylorrhynchus heterochaetus

【Objective】Simple sequence repeat(SSR) loci were detected and characterized in the transcriptome of Tylorrhynchus heterochaetus,the distribution pattern was analyzed to provide reference for the efficient development of SSR markers. 【Method】The transcriptomic data of T. heterochaetus were obtained by high-throughput sequencing technology.After filtering and assembly, the SSR loci were searched and identified by MISA, and their characteristics and distribution were analyzed. The effectiveness of SSR primers was preliminarily verified, and the polymorphism of effective amplification primers was further analyzed. 【Result】Transcriptome assembly generated 79420 Unigenes(total length 104411064 bp) with a N50 length of 1902 bp and a N90 length of 331 bp. From the 79420 Unigenes, a total of 9932 SSR loci were detected and distributed on 8707 Unigenes,with SSR existence frequency of 8.49% and an occurrence frequency of 7.43%. Of which,1029 Unigenes contained more than one locus,and the SSR abundance reached 58.85 loci/Mb(single nucleotide repeats were not included). A total of 133 SSR repeat types were observed and the number of repetition ranged from 4 to 26,most of which were 4 to 15. About 20% of the SSR loci were found to be ≥20 bp in length. The dominant repeat units were dinucleotide,mononucleotide and trinucleotide,which accounted for 40.29%,32.12% and 21.76% of the total SSR loci respectively. The AT/TA was the dominant repeat unit in dinucleotide,accounting for 79.88% of this type SSR loci. The A/T and AGG/CCT were the main repeat units in mononucleotide and trinucleotides,accounting for 65.92%and 29.06% respectively. In addition,7296(80% of the total SSR) type Ⅱ SSR loci with medium polymorphism were found to be predominant,and the remaining 1813(20% of the total SSR) SSR loci were type I with high polymorphism. A total of 11 pairs of SSR primers were validated to be polymorphic,and the average number of alleles per primer pair reached 3.73. 【Conclusion】The SSR loci in the transcriptome of T. heterochaetus have a rich variety and high polymorphic potential. They can be used for the development of SSR molecular markers and has practical value for the evaluation,protection and utilization of germplasm resources and the study of population genetics and molecular breeding.