SSR， SNP and InDel characteristics analysis based on transcriptome of Bougainvillea glabra‘Elizabeth Angus’

【Objective】The characteristics of SSR， SNP and InDel sites in Bougainvillea glabra ‘Elizabeth Angus’ were analyzed based on transcriptome sequencing data to provide theoretical basis for developing molecular markers， breeding thornless or less thorn varieties， variety identification and kinship analysis of B. spectabilis Willd. 【Method】The branch thorn and stem segment at three development stages of B. glabra‘ Elizabeth Angus’ were used to transcriptomed， The obtained high-quality sequencing data were sequenced and assembled by Trinity， and SSR， SNP and InDel were characterized using MISA and GATK3. 【Result】A total of 45905982 bp raw data were obtained from the transcriptome of 18 samples， and 45640193 bp clean data were obtained after quality control filtration. 312812 transcripts and 144512 unigenes were obtained after splicing， and 54516 SSR sites were distributed on 40820 unigenes， the frequency was 28.25%， the average distance was 2.67 kb， and 10269 unigenes contained more than one SSR locus， accounting for 4.25% of the total number of unigenes. Among the repeat unit types， the numbers of mononucleotide， dinucleotide and trinucleotide repeats were dominant， mononucleotide type had the largest number of repeat motifs （39904，73.20%） ， the second was dinucleotide repeats （8169，14.98%） and trinucleotide repeats （5899，10.82%）， the pentanucleotide repeats was the least （31，0.06%）. A total of 98 repetitive motifs were detected from mononucleotide to hexanucleotide repeat types， with an occurrence frequency of 0.01%-25.71%. Among them， the most frequent motif was A/T （37151）， accounting for 68.15% of the total SSR sites. The motif repeats of SSR mainly concentrated in 5-23 times and the length of SSR sequences was mainly 10-60 bp， the average length was 20.38 bp. A total of 231248 SNP sites and 99580 InDel sites were detected， with an average distribution distance of 1.59 kb SNP site and 0.68 kb InDel site respectively， and the number of unigenes contained one site was the largest， and the number of unigenes gradually decreased with increa-sing the number of SNP and InDel sites.【 Conclusion】B. glabra‘ Elizabeth Angus’ transcriptome has abundant SSR sites， rich types and obvious distribution characteristics， which can be used to develop a large number of SSR markers. SNP and InDel sites occur less frequently than model plants， which requires further mining.