木薯EST资源的SSR信息分析

Analysis of SSR informa tion in EST resource of cassava

为了进一步利用现有木薯EST-SSR资源,笔者从NCBI公共数据库下载了38411条木薯EST,去除低质量的和冗余的的序列后,得到全长为4.16×103kb的无冗余序列5401条。在无冗余序列中发现含有SSR的EST序列595条,共691个SSR,平均相隔6.02kb出现一个SSR。这些SSR的出现频率和平均长度分别是11.02%和18.89bp。在1～6bp的重复基元中,二核苷酸重复基元出现频率最高(36.03%),其次是三核苷酸重复基元(31.84%)、单核苷酸重复基元(30.10%)。出现较多的重复基元是A/T(29.23%),其次是AG/CT(24.75%)。结果说明,木薯的EST-SSR出现频率较高、类型较丰富、多态性潜能较高,具有较高的利用价值。

To utilize farther the EST - SSR resources of cassava.38411 EST of cassava in the database of NCBI were downloaded and analysed, resulting in 5401 non-redundant EST with total length about 4.16x103 kb. Among them there were 595 microsatellite sequences containing 691 EST-SSR, which amounted to 11.02% of the non-redundant starting sequence population. The average length and distribution distance of the EST- SSRs were about 18.89 bp and 6.02 kb respectively. Among the different motifs ranging from 1 to 6 bp, dinucleotide repeats were most abundant （36.03%）, followed by trinucleotide repeats （31.84%） and mononucleotide repeats （30.10%）. Among all identified motif types, A/T had the high EST frequency （29.23%）, followed by AG/CT （24.75%）. The result in this paper indicated that the EST - SSR of cassava had comparably high utility value.