摘要
从NCBI公共数据库获得262 113条甘蔗EST,通过前处理和聚类拼接得到全长为50 058.89 kb的无冗余Unigene 62 565条。在这些序列中搜索出9 482个SSRs,出现频率是15.15%;平均5.28 kb出现1个SSR。三核苷酸重复是主要的类型,占总SSRs的45.92%。CT和CGC是二、三核苷酸中的优势重复类型,分别占二、三核苷酸重复的21.22%和8.18%。此外还对筛选出的SSR进行多态性预测,得到了长度在20 bp以上的低级基元一、二、三核苷酸EST-SSR共1 405条,占长度20 bp以上的SSR总数的59.16%。结果为甘蔗EST-SSR标记的开发和相关分子生物学研究提供资料和奠定基础。
Expressed sequence tags（ESTs） offer the opportunity to exploit single,low-copy,conserved sequence motifs for the development of simple sequence repeats（SSRs）.The total of 262 113 ESTs of sugarcane（Saccharum officinarum） in the database of NCBI were downloaded and analyzed,which resulted in 62 565 non-redundant Unigenes with total length about 50 058.89 kb.9 482 SSRs from these sequences were acquired.The frequency of SSR in the unigene was 15.15%.One piece of SSR arised in 5.28 kb averagely.Trinucleotide repeats were the main type,accounting for 45.92% of the total SSRs.The dominant repeats types were dinucleotide and trinucleotide,accounting for 21.22% and 8.18% respectively.The polymorphism of SSRs was assessed.The searching and analysis of SSRs lays foundations for the exploitation of sugarcane EST-SSR tags and the related research of molecular biology.
出处
《热带作物学报》
CSCD
2010年第9期1497-1501,共5页
Chinese Journal of Tropical Crops
基金
现代农业产业技术体系建设专项资金(No.nycytx-024)
国家948项目(2010-C21)资助
关键词
甘蔗
表达序列标签
简单重复序列
特性
Sugarcane
Expressed sequence tag （EST）
Simple seuqence repeat （SSR）
Characteristics
