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利用Trinity软件对白姜转录组进行de novo组装,CAP3软件对组装的contig拼接删选;MISA工具对unigene进行SSR检索。从153 724条unigene中共发现16 593个SSR,分布在14 436条unigene序列中,出现频率为9.39%,平均每9.26kb含有1个SSR位点。其中二核苷酸、三核苷酸所占比例最大,分别为37.59%和45.24%;二者分别以AG/CT和AGG/CCT重复基元为主,占22.47%和11.79%。基序长度主要分布于12~20bp,占总数的85.06%。研究结果表明,白姜SSR位点频率、密度较高,类型多样,在生姜分子标记辅助育种、遗传多样性研究中有较大应用潜能。
De novo assembly of white ginger transcriptome using Trinity software, contig splicing deletion of CAP3 software assembly, and unigene SSR search using MISA tool. A total of 16 593 SSRs were found from 153 724 unigene distributions in 14 436 unigene sequences with a frequency of 9.39% and an average of one SSR locus per 9.26 kb. Among them, dinucleotide and trinucleotide accounted for the largest proportion, accounting for 37.59% and 45.24% respectively. The two were mainly AG / CT and AGG / CCT repeat elements, accounting for 22.47% and 11.79% respectively. The length of motif is mainly distributed in 12 ~ 20bp, accounting for 85.06% of the total. The results showed that the SSR locus of G. glutinosa had higher frequency, higher density and different types, and had great potential in molecular marker-assisted breeding and genetic diversity of ginger.