Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases
Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases
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DOI：
10.1007/s00122-001-0849-1
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发表时间：
2002-04-01
影响因子：
5.4
通讯作者：
Dubcovsky, J
中科院分区：
文献类型：
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作者：
Echenique, V;Stamova, B;Dubcovsky, J
使用BLASTSearch搜索估计国际小麦族EST联盟（ITEC）数据库（61，942个序列：82%小麦、10%大麦、8%黑麦）和DuPont EST数据库（86，628个小麦序列）中Ty 1-copia型和Ty 3-gypsy型反转录转座子的频率。这些ESTs从94个来自不同组织（叶、根、穗、花和种子）和不同生长条件的cDNA文库中获得，不包括消减和归一化cDNA文库。小麦EST数据库筛选使用4个不同的Ty 1-copia型，12个逆转录酶序列，和三个Ty 3-gypsil型小麦反转录转座子序列。使用BLAstem评分高于100或E值小于e（-20）的选择阈值，发现0.145%的EST与搜索中使用的至少一种反转录转座子显著相似（0.064%Ty1-copia，0.081%Ty3-gypsv）。当BLACKS阈值变为E时，该百分比增加至0.176
The frequency of Ty1-copia-type and Ty3-gypsy-type retrotransposons in the International Triticeae EST Consortium (ITEC) database (61,942 sequences: 82% wheat, 10% barley, 8% rye) and the DuPont EST database (86,628 wheat sequences) was estimated using BLASTN searches. These ESTs were obtained from 94 cDNA libraries from different tissues (leaves, roots, spikes, flowers and seeds) and different growing conditions, excluding subtracted and normalized cDNA libraries. Triticeae EST databases were screened using four different Ty1-copia-type, 12 reverse transcriptase sequences, and three Ty3-gypsil-type Triticeae retrotransposon sequences. Using a selection threshold of BLASTN scores higher than 100 or E values smaller than e(-20), 0.145% of the ESTs were found to be significantly similar to at least one of the retrotransposons used in the search (0.064% Ty1-copia, 0.081% Ty3-gypsv). This percentage increased to 0.176% when the BLASTN threshold was changed to E