摘要
为充分利用现有公共数据库中的EST资源开发EST-SSR引物,本研究从GenBank数据库获取39 227条油棕EST,通过聚类拼接和处理,得到全长为7 977.734 kb的无冗余序列15 716条。在这些序列中共检索出699个SSRs,检出率为4.45%,平均11.41 kb出现1个SSR,包括99种重复基元。其中,二核苷酸和三核苷酸重复是主要的类型,分别占总SSRs的38.48%和25.32%。在所有的核苷酸重复基序中,二核苷酸重复序列AG/CT所占比例最高,约占27.47%。Blastx分析发现44.95%的SSR-ESTs与非冗余蛋白质序列数据库(nr)中功能基因同源,功能已知的蛋白质中葡萄来源的SSR-ESTs所占比例最大,为4.42%。同时对54条SSR-ESTs通过GO体系进行功能分类,其中46条能找到同源物,其余8条无同源物,这些序列可划分为18个亚类,在所有功能亚类中,结合活性的功能项和SSR-ESTs数量最多,另外580条未被注释功能信息。
In order to make full use of the EST resources in the present public database to develop the EST-SSR primers,in this study,39 227 ESTs of oil palm（Elaeis guineensis Jacg.） from GenBank database were downloaded and analyzed,resulting in 15 716 non-redundant sequences with total length about 7 977.734 kb.699 SSRs were discovered,the frequency of these EST-SSRs was 4.45% and the mean distance was 11.41 kb in non-redundant ESTs.Among them the dinucleotide and trinucleotide repeats were dominant types,accounting for 38.48% and 25.32% respectively.AG/CT was repeated most in all nucleotide repeat motifs,accounting for 27.47%.Blast analysis showed that 44.95% of SSR-ESTs were homologous with functional gene in non-redundant protein sequences databases（Nr database）.The homology with known functions from Vitis vinifera had the greatest proportion and reached up to 4.42%.Simultaneously,the functional classification of 54 SSR-ESTs as made by GO system,of which 46 were found in the Nr and EST database,and the other 8 showed no homology.These ESTs can be divided into 18 functional subclasses,and the functional items and SSR-ESTs relevant to binding presented higher quantity than all other functional subclasses.The function of other 580 ESTs was not researched.
出处
《中国油料作物学报》
CAS
CSCD
北大核心
2012年第1期101-105,共5页
Chinese Journal of Oil Crop Sciences
基金
国家天然橡胶产业体系(nyhyzx07-033-1)
海南省自然科学基金(809031)
