摘要
利用MISA软件对密花香薷转录组42362条Unigene进行SSR位点搜索,并对其SSR序列结构及分布特征进行了分析。结果表明:(1)密花香薷转录组Unigene序列中共检测到17564个SSR重复序列,分布于11903条Unigene上,出现频率为28.10%,平均每3200 bp出现一个SSR位点。(2)单、二、三核苷酸重复类型为密花香薷转录组SSR位点的主导基序类型,占总SSR位点的97.27%,3种主导基序类型中,单核苷酸所形成基元类型数量最多,共检测到169个基元类型(51.22%),单核苷酸(A/T)n基元类型占明显优势,二核苷酸重复类型(AG/CT)n基元类型占优,分别占总SSR位点的50.60%和12.17%。(3)单核苷酸SSR位点所包含重复次数最多(49),重复次数介于10~66,同一基序类型不同重复次数所形成的SSR位点数量差异较大,随重复次数的增加,SSR位点数呈下降趋势。(4)密花香薷转录组二至六核苷酸基序SSR序列长度集中在12~30 bp区间,共包含有8190个SSR位点,占所统计SSR位点的95.60%,1589(≥20 bp)个SSR序列具有极高的多态性,占所统计SSR位点的18.54%。综合出现频率、分布密度、基元重复次数和长度变异等多个研究结果发现,密花香薷转录组检索到的SSR序列表现出较高的多态性潜能,具有较大的开发价值。该研究为后续密花香薷SSR分子标记引物开发奠定了理论基础。
The SSR loci which exist in 42362 Unigenes in Elsholtzia densa transcriptome were detected by MISA software,additionally,the structure and distribution characteristics were analysed.The results indicated that:(1)a total of 17564 SSR repeating sequences have been searched,which were distributed on 11903 Unigenes,and the frequency of occurrence of SSR loci was 28.10%with an average of one SSR locus per 3200 bp.(2)The dominant repeat motifs in Elsholtzia densa transcriptome were mono-nucleotide,di-nucleotide and tri-nucleotide,accounting for 97.27%of the total SSR loci,and among the three dominant motif types,the number of motif type formed by mono-nucleotide was the largest with a total of 169 motif types(51.22%),the(A/T)n in mono-nucleotide repeats and(AG/CT)n in di-nucleotide repeats,were dominating motifs,accounting for 50.60%and 12.17%,respectively.(3)The mono-nucleotide motif was the type which repeated the most(49),the repetition times were between 10 and 66,and the difference of the SSR number was widely showed in the same motif with different repetition,the number of SSR was declined as the increase of repetition times.(4)The length of SSR was concentrate on a range from 12 to 30 bp which contained a total of 8190 SSR loci,accounting for 95.60%of the total SSR in di-nucletide to six nucleotide motifs,and the number of highly polymorphic SSR sequences was 1589(≥20 bp)which accounting for 18.54%of the total SSR.The SSR sequences showed higher potential polymorphism and greater value for development,based on the results of multiple studies,such as occurrence frequency,distribution density,motif repetition and length variation.This study laid a theoretical foundation for the development of SSR primers in a follow-up studies for Elsholtzia densa.
作者
富贵
刘玉萍
苏旭
FU Gui;LIU Yuping;SU Xu(Qinghai Provincial Key Laboratory of Highvalue Utilization of Characteristic Economic Plants, College of Ecological Environment and Resources, Qinghai Nationalities University, Xining 810007, China;2College of Life Science, Qinghai Normal University, Xining 810008, China;3Academy of Plateau Science and Sustainability, Xining 810016, China)
出处
《西北植物学报》
CAS
CSCD
北大核心
2021年第4期654-663,共10页
Acta Botanica Boreali-Occidentalia Sinica
基金
2021年青海民族大学校级规划项目(2021XJGH14)。
关键词
转录组
密花香薷
SSR
位点信息
transcriptome
Elsholtzia densa
SSR
loci information
