EST-STR MINING FROM DENDROBIUM NOBILE
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摘要: 金钗石斛是常见的药用和花卉植物，但是缺乏在基因组尺度上对该物种的研究.本研究利用计算机程序搜索了金钗石斛EST上的短串联重复位点，共获得2 122个基序长度2～7bp,STR长度不小于12bp且重复次数不小于3的STR位点. 其中，3bp-STR最为丰富，而 2bp和6bp基序的STR位点也在可表达基因中富集.一般而言，随着基序长度的增加，STR的重复次数和分布范围减少/缩窄. 金钗石斛基因组上存在439个基因特异分布的STR位点，暗示这些STR位点可能与特定的功能基因共进化.
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关键词:
- 金钗石斛，短串联重复，表达序列标签
Abstract: Dendrobium nobile is a herb and floral plant, but the studies at the genomic scale on this species are rare. Through the computer-facilitated data mining, a total of 2122 short tandem repeat (STR) loci that contain motifs in length ranged from 2bp to 7bp and with 3 or more repeats were identified from an EST collection of Dendrobium nobile . Analysis on the STR frequency indicates that group of 3bp-STR is most abundant, while those with 2bp- and 6bp-motif also enriched in expressed genes. Generally, the number of repeats and the distribution range of STRs decreases with the length of motif. A total of 439 STRs are gene-specific hosted, suggesting a co-evolution between these STR loci and the specific functional genes. These results will facilitate the comparative studies between Dendrobium nobile and other plants at the genomic scale. -
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