基于RNA-seq的两种柳树转录组微卫星特征比较分析

Comparison of Microsatellites Characteristics of Two Salix Transcriptome Based on RNA-seq

随着高通量测序技术的飞速发展,转录组测序为EST-SSR标记的开发提供了重要的信息资源。为阐明柳树中EST-SSRs的变化情况,本研究以垂柳和簸箕柳转录组序列为来源,分析并比较了两种柳树中EST-SSR的分布规律及特征。结果表明:垂柳与簸箕柳中EST-SSR发生频率分别为3.6%和4.8%,SSR的重复数量和碱基类型呈负相关,而重复数量与EST-SSR总长度或EST-SSRs总数量呈正相关。二、三碱基重复在两种柳树中均为主要类型,三碱基重复占比最大(垂柳为47.5%,箕柳簸为47.8%),五碱基重复占比最小(垂柳为2.4%,簸箕柳为1.9%)。两种柳树中,(AG/CT)、(AAG/CTT)、(AAAT/ATTT)和(AAAAG/CTTTT)分别为不同碱基重复中最丰富的基元类型,而(AAACCG/CGGTTT)和(AGAGGG/CCCTCT)分别为垂柳和簸箕柳六碱基重复中最主要类型。通过侧翼序列分析,EST-SSR趋向产生于A/T富集区域。此外,共有1 305个垂柳EST-SSR和2 463个簸箕柳EST-SSR被成功定位到毛果杨染色体上。本研究将为后期柳树EST-SSR标记的开发及分子遗传学的研究提供科学依据。

With the rapid development of high-throughput sequencing techniques, RNA-seq provides valuable information resources of expressed sequence tags(ESTs) for developing SSRs. To investigate the variation of EST-SSRs in Salix, the transcriptome sequences of S. babylonica and S. suchowensis were selected as research sources and the distribution rules and characteristics of EST-SSR in two Salix were analyzed and compared. The results indicated that the occurrence frequency of EST-SSR in S. babylonica and S. suchowensis were 3.6% and 4.8%, respectively. The correlation between the repeat number and the motif type was negative, while the correlation between the repeat number and the full length of EST-SSR or the total number of SSRs was positive.Di-nucleotide and tri-nucleotide repeats were the most abundant motif types in two Salix. The proportion of tri-nucleotide repeats was the largest(47.5% for S. babylonica and 47.8% for S. suchowensis), while the proportion of penta-nucleotide repeats was the least(2.4% for S. babylonica and 1.9% for S. suchowensis). AG/CT, AAG/CTT,AAAT/ATTT and AAAAG/CTTTT were the most abundant di-, tri-, tetraand penta-nucleotide repeat motifs in S.babylonica and S. suchowensis, respectively. AAACCG/CGGTTT and AGA GGG/CCCTCT were the most frequent hexa-nucleotide repeat motifs in S. babylonica and S. suchowensis, respectively. Through the analysis of flanking sequences, EST-SSRs tended to occur in A/T-rich regions. Furthermore, 1 305 EST-SSRs from S.babylonica and 2 642 EST-SSRs from S. suchowensis were successfully mapped onto chromosomes of Populus trichocarpa. This study might provide scientific reference for the development of EST-SSR markers and the research on molecular genetics in Salix.