Ralph Steven, Oddy Claire, Cooper Dawn, Yueh Hesther, Jancsik Sharon, Kolosova Natalia, Philippe Ryan N, Aeschliman Dana, White Rick, Huber Dezene, Ritland Carol E, Benoit François, Rigby Tracey, Nantel André, Butterfield Yaron S N, Kirkpatrick Robert, Chun Elizabeth, Liu Jerry, Palmquist Diana, Wynhoven Brian, Stott Jeffrey, Yang George, Barber Sarah, Holt Robert A, Siddiqui Asim, Jones Steven J M, Marra Marco A, Ellis Brian E, Douglas Carl J, Ritland Kermit, Bohlmann Jörg
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3.
Mol Ecol. 2006 Apr;15(5):1275-97. doi: 10.1111/j.1365-294X.2006.02824.x.
As part of a genomics strategy to characterize inducible defences against insect herbivory in poplar, we developed a comprehensive suite of functional genomics resources including cDNA libraries, expressed sequence tags (ESTs) and a cDNA microarray platform. These resources are designed to complement the existing poplar genome sequence and poplar (Populus spp.) ESTs by focusing on herbivore- and elicitor-treated tissues and incorporating normalization methods to capture rare transcripts. From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139,007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385,000 publicly available Populus ESTs. Clustering and assembly of 107,519 3'-end ESTs resulted in 14,451 contigs and 20,560 singletons, altogether representing 35,011 putative unique transcripts, or potentially more than three-quarters of the predicted c. 45,000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15,496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up-regulated, compared to only 537 down-regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1-aminocyclopropane-1-carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (-)-germacrene D synthase] and transcriptional regulation [e.g. leucine-rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for functional investigation of plant-insect interactions in poplar.
作为杨树中针对昆虫食草作用的诱导防御特性进行基因组学研究策略的一部分，我们开发了一套全面的功能基因组学资源，包括cDNA文库、表达序列标签（EST）和一个cDNA微阵列平台。这些资源旨在通过聚焦于经食草动物和激发子处理的组织，并采用标准化方法来捕获稀有转录本，从而补充现有的杨树基因组序列和杨树（胡杨属）EST。从15个标准、标准化或全长cDNA文库中，我们生成了139,007个3'或5'端测序的EST，占约385,000个公开可得的杨树EST的三分之一以上。对107,519个3'端EST进行聚类和组装，得到了14,451个重叠群和20,560个单拷贝序列，总共代表35,011个假定的独特转录本，或可能超过杨树基因组中预测的约45,000个基因的四分之三。利用这一EST资源，我们开发了一个包含15,496个独特基因的cDNA微阵列，用于监测杨树叶片在受到森林天幕毛虫（Malacosoma disstria）食草作用后的基因表达。取食后经过24小时，1191个基因被归类为上调，相比之下只有537个基因下调。对这个诱导基因集的功能分类揭示了在植物防御（如内切几丁质酶、库尼茨蛋白酶抑制剂）、十八烷酸和乙烯信号传导（如脂氧合酶、丙二烯氧化物合酶、1-氨基环丙烷-1-羧酸氧化酶）、转运（如ABC蛋白、钙网蛋白）、次生代谢[如多酚氧化酶、异黄酮还原酶、（-）-吉马烯D合酶]和转录调控[如富含亮氨酸重复跨膜激酶、几类转录因子（锌指C3H型、AP2/EREBP、WRKY、bHLH）]中发挥作用的基因。本研究提供了首个在木本多年生植物中表征昆虫诱导防御的全基因组规模方法，为杨树中植物 - 昆虫相互作用的功能研究提供了坚实平台。
