基于转录组数据的直立型扁蓿豆SSR序列特征分析

Analysis of SSR characteristics for Medicago ruthenica‘Zhilixing’based on transcriptome data

【目的】对直立型扁蓿豆转录组简单重复序列(SSR)特征进行分析,为开发扁蓿豆新的分子标记奠定基础。【方法】以直立型扁蓿豆叶片为材料,通过Illumina HiSeq X Ten测序平台进行高通量测序,利用MISA软件对转录组数据进行SSR位点搜索,并对SSR位点的分布及其序列特征进行分析。【结果】在直立型扁蓿豆中得到308449条参考序列(Unigene),从中挖掘到89688个SSR位点,SSR出现频率为29.08%,平均分布距离3.17 kb。SSR重复基元数量以单核苷酸为主(53710个SSR,占比59.89%),三核苷酸(18586个SSR,占比20.72%)、二核苷酸(15446个SSR,占比17.22%)次之。在159种重复基元中,单核苷酸A/T类型占比最高(58.50%),其次为二核苷酸AG/CT基元(8.29%)。直立型扁蓿豆转录组SSR以6~15次重复为主,6种核苷酸重复类型数量总体表现为随着基元重复次数的增加而减少。SSR长度主要集中在12~120 bp,此长度范围SSR数量占SSR总数的41.62%,具有较高多态性潜能的SSR(长度>20 bp)位点数为20557,占比22.92%。【结论】直立型扁蓿豆SSR位点出现频率高、基元重复类型丰富、多态性潜能高,在扁蓿豆遗传多样性与品种分子鉴定及新的分子标记开发等方面具有较大的应用价值。

【Objective】This study analyzed the SSR characteristics of leaf transcriptome of Medicago ruthenica‘Zhilixing’to establish new molecular markers.【Method】High-throughput sequencing for lea-ves petals of Medicago ruthenica‘Zhilixing’was performed with the Illumina HiSeq X Ten sequencing.The software MISA was used to explore all SSR loci in the transcriptome database of Medicago ruthenica‘Zhilixing’and the SSR characteristics were analyzed.【Result】A total of 89688 SSR loci were mined from 308449 reference sequences(Unigene)of Medicago ruthenica‘Zhilixing’with frequency of 29.08%and average distribution distance of 3.17 kb.Most repeat motifs were mono-nucleotide motifs(53710,59.89%),followed by tri-nucleotide motifs(18586,20.72%)and di-nucleotide motifs(15446,17.22%).Among the 159 repetitive motifs,the mono-nucleotide A/T type had the highest ratio of 58.50%,followed by the di-nucleotide AG/CT motif(8.29%).In addition,the SSR of the Medicago ruthenica‘Zhilixing’transcriptome was dominated by 6-15 repetitions,and the number of 6 nucleotide repeat types generally decreased with the increase of motif repetitions.The length of SSR was mainly concentrated in 12-120 bp with ratio of 41.62%.The number of SSR loci(length>20 bp)with high polymorphism potential was 20557 and the proportion was 22.92%.【Conclusion】The SSR locus of Medicago ruthenica‘Zhilixing’had high occurring frequency,rich motif repeat types and high polymorphism potential.It showed great application value in genetic diversity,molecular identification of varieties and development of new molecular markers for Medicago ruthenica.