Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis
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摘要: 为利用微卫星分子标记技术进一步研究油松胚珠发育分子调控机制以及微卫星对油松胚珠发育的影响,本文以前期高通量测序结果为基础,用MISA软件对所获得的转录组数据进行SSR位点的发掘和分析,为后续研究提供重要信息资源和数据保障。得到的1412个SSR位点存在于1274条序列中,平均每2.15kb出现一个SSR。油松胚珠转录组微卫星中存在87种重复基元,其中(A/T)n比例最高,约占45.89%;出现频率较高的重复类型是单核苷酸(46.88%)和三核苷酸(34.99%)重复。所得微卫星多为长度<20bp的短重复序列,≥20bp仅占总数的5.67%,重复序列出现频率与长度呈负相关。所得的SSR位点大部分位于非编码区,位于编码区的仅232个,有18个跨越了编码区和非编码区;编码区中占比例最高的是三核苷酸重复序列(105个,45.26%)。Abstract: In order to understand the molecular mechanism of regulating ovule development of Pinus tabulae-formis thoroughly and clarify the influence of microsatellites in ovule development, we used the program MISA to mine and analyze the high-throughput sequencing in earlier experiments to seek the microsatellites of transcriptome, in an attempt to provide significant information and data for deeper research. A total of 1412 SSRs were identified in 1274 unigenes with one SSR per 2.15kb. Among 87 SSR repeat motifs of ovule transcriptome, (A/T)n was in the maximum proportion, accounting for 45.89%. Mononucleotide and trinucleotide repeats were the two more abundant in all repeat types, accounting for 46.88% and 34.99%, respectively. The microsatellites with length below 20 bp were in the majority and those over 20 bp amounted only 5.67%. It showed a negative relation between the frequency of occurrences and the length of microsatellites. Most of SSRs were in untranslated region, and only 232 SSRs were located in protein-coding regions, while 18 in both of them. Trinucleotide repeats were the richest in protein-coding regions (105, 45.26%).
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Keywords:
- Pinus tabulaeformis /
- ovule /
- transcription /
- microsatellite
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