Comparative analyses of potato expressed sequence tag libraries
Comparative analyses of potato expressed sequence tag libraries
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DOI：
10.1104/pp.013581
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发表时间：
2003-02-01
期刊：
影响因子：
7.4
通讯作者：
Buell, CR
中科院分区：
文献类型：
--
作者：
Ronning, CM;Stegalkina, SS;Buell, CR
栽培马铃薯（Solanum tuberosum）与茄科的其他成员具有相似的生物学特性，但在该家族中具有独特的特征，例如发育成可食用块茎的改性茎（匍匐茎）。为了更好地了解马铃薯生物学，我们进行了调查的马铃薯转录组表达序列标签（EST）从不同的组织。从地上组织、地下组织和用晚疫病病原体（致病疫霉）攻击的组织中总共产生了61，940个EST。这些EST的聚类和组装导致总共19，892个独特序列，其中8，741个暂定共有序列和11，151个单ESTs。我们能够确定这些序列的43.7%的推定功能。许多序列（48）在整个取样的文库中表达，代表组成型表达的序列。其他序列（13，068，21%）是唯一表达的，仅在单个文库中检测到。利用EST序列的层次和k均值聚类，我们能够将基因表达的变化与马铃薯生物学中的主要生理事件相关联。利用成对比较块茎相关组织，我们能够关联基因与块茎的启动，休眠和发芽。我们还能够鉴定出一些特征性的以及新的序列，这些序列是晚疫病病原体不相容相互作用所特有的，从而为进一步了解抗性机制提供了基础。
The cultivated potato (Solanum tuberosum) shares similar biology with other members of the Solanaceae, yet has features unique within the family, such as modified stems (stolons) that develop into edible tubers. To better understand potato biology, we have undertaken a survey of the potato transcriptome using expressed sequence tags (ESTs) from diverse tissues. A total of 61,940 ESTs were generated from aerial tissues, below-ground tissues, and tissues challenged with the late-blight pathogen (Phytophthora infestans). Clustering and assembly of these ESTs resulted in a total of 19,892 unique sequences with 8,741 tentative consensus sequences and 11,151 singleton ESTs. We were able to identify a putative function for 43.7% of these sequences. A number of sequences (48) were expressed throughout the libraries sampled, representing constitutively expressed sequences. Other sequences (13,068, 21%) were uniquely expressed and were detected only in a single library. Using hierarchal and k means clustering of the EST sequences, we were able to correlate changes in gene expression with major physiological events in potato biology. Using pair-wise comparisons of tuber-related tissues, we were able to associate genes with tuber initiation, dormancy, and sprouting. We also were able to identify a number of characterized as well as novel sequences that were unique to the incompatible interaction of late-blight pathogen, thereby providing a foundation for further understanding the mechanism of resistance.