松属编码区微卫星特征和相应基因功能分析

从GenBank下载453 892条松属EST序列,序列组装后得到20 886条contig。用Sputnik软件从这些contig中查找了2 678个微卫星,其中3碱基重复微卫星占的比例最高,为59.2%,而其他重复长度的微卫星都相对较低,比例分别为:2碱基重复微卫星占12.0%,4碱基重复微卫星占13.3%,5碱基重复微卫星占15.5%。3碱基重复微卫星变化引起的基因读码框改变最小,松属树种基因区3碱基重复微卫星的富集显示了强烈的密码子选择效应。此次研究还对查找到的微卫星进行了引物设计和扩增分析。实验结果显示,设计的微卫星引物在云南松中的扩增成功率是72.9%。从扩增成功的引物中进一步选取了155对引物,对14个松属树种和1个黄杉属树种进行了引物通用性实验分析,结果显示155对引物在14个松属树种间的通用性在71.0%以上,而在黄杉属树种中的通用性只有25.2%。对松属树种中含有微卫星的基因进行了功能分类研究,结果显示基因在是否保留微卫星序列方面有显著分化,微卫星参与了如细胞成分分类的共质体组成、病毒颗粒及病毒颗粒组成、生物节律调控, 以及生长素转运蛋白等生物学过程。

Characterization of microsatellites in coding genes and functional analysis of these genes in pines

In this study, 453 892 Pinus ESTs were downloaded from GenBank, and these ESTs were assembled into 20 886 contigs(representing 20 886 unigenes of pines)with GS De novo assembler from roche, according to species, respectively. Searching by the Sputnik engine, 2 678 microsatellites were detected in the assembled contigs. It is noticeable that trinucleotide repeats were found to be the most abundant microsatellites in this database(accounting for 59.2%). By contrast, the richness of the other type of microsatellites were relatively low, with di-, tetra-, penta-nucleotide repeats accounted for 12.0%, 13.3% and 15.5% of the detected microsatellites, respectively. Dominance of triplet microsatellites in genes can be well interpreted by genetic codon selection, since triplet corresponds to the length of genetic codon. Insertion or deletion of integrate genetic codon influences the protein less slightly than the insertion or deletion of other types of repeats. Experimental results showed an overall amplification successful rate about 72.9% in P. massoniana. Subsequently, 155 successfully amplified primer pairs were tested for transferability across 14 pine species and in Douglas fir. This test yielded transferability rates over 71.0% across the 14 pine species, yet it was only 25.2% in Douglas fir. In genus Pinus, functional analyses indicated that genes with and without SSRs were significantly diverged in categories of symplast, virion and virion part classified by cellular component, in rhythmic process category classified by biological process, and in auxiliary transport protein category classified by molecular function.