蔡年辉, 许玉兰, 徐杨, 邓丽丽, 周丽, 王大玮, 何承忠, 段安安. 云南松转录组SSR的分布及其序列特征[J]. 云南大学学报(自然科学版), 2015, 37(5): 770-778. doi: 10.7540/j.ynu.20150206
引用本文: 蔡年辉, 许玉兰, 徐杨, 邓丽丽, 周丽, 王大玮, 何承忠, 段安安. 云南松转录组SSR的分布及其序列特征[J]. 云南大学学报(自然科学版), 2015, 37(5): 770-778. doi: 10.7540/j.ynu.20150206
CAI Nian-hui, XU Yu-lan, XU Yang, DENG Li-li, ZHOU Li, WANG Da-wei, HE Cheng-zhong, DUAN An-an. The distribution and characteristics of SSR in transcriptome of Pinus yunnanensis[J]. Journal of Yunnan University: Natural Sciences Edition, 2015, 37(5): 770-778. DOI: 10.7540/j.ynu.20150206
Citation: CAI Nian-hui, XU Yu-lan, XU Yang, DENG Li-li, ZHOU Li, WANG Da-wei, HE Cheng-zhong, DUAN An-an. The distribution and characteristics of SSR in transcriptome of Pinus yunnanensis[J]. Journal of Yunnan University: Natural Sciences Edition, 2015, 37(5): 770-778. DOI: 10.7540/j.ynu.20150206

云南松转录组SSR的分布及其序列特征

The distribution and characteristics of SSR in transcriptome of Pinus yunnanensis

  • 摘要: 分析云南松转录组中的SSR位点信息的分布及其序列特征,为SSR引物的开发做前期工作.从80000条转录组Unigene序列中,搜索到2455个SSR,出现频率为3.07%,分布的平均距离29 kb.SSR以三、二核苷酸占优势,分别占总数42.73%和27.25%,而以四核苷酸的较少,仅占总数的0.98%.重复片段长度12~25bp,其中近90%的集中在12~20bp,平均16.09bp.AT/AT与AGC/CTG和AAG/CTT为二、三核苷酸优势重复基元,分别占基元总数的16.66%、9.65%和8.39%.从2899对引物中随机挑选32对引物用于检测,24对成功扩增.云南松转录组SSR位点出现的频率较高,分布距离较近,基元类型丰富,重复次数较高,具有较高的多态性潜力.云南松转录组产生的Unigene是开发SSR的有效来源,获得的SSR引物可为云南松种质资源的遗传变异研究提供更多的标记.

     

    Abstract: In total 80000 Unigenes from needle transcriptome of Pinus yunnanensis Franch. 2455 SSRs identified were screened using MISA software and identified.The frequency of SSR was 3.07% and mean distribution density was 29 kb.Tri-nucleotide and di-nucleotide were major repeated types,accounting for 42.73% and 27.25%,respectively.Tetranucleotide was minimum (0.98%).AT/AT,AGC/CTG and AAG/CTT were respectively most frequent repeated motifs in di-nucleotide and tri-nucleotide repeated types,and accounting for 16.66%,9.65% and 8.39%.SSR primers were designed based on these Unigenes.24 primers were successfully amplified out of 32 primers which were selected randomly from 2899 primers.The SSR loci in the P.yunnaensis transcriptome showed moderate frequency of distribution,close distribution distance,rich repeated types,high repeated times and significant potention of polymorphism.The results indicated that the Unigenes obtained from transcriptome sequence in P.yunnanensis can be used as an effective way for the development of SSR loci.The SSR primers will provide more markers for the research of genetic variation of P.yunnanensis.

     

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