Genome organization of more than 300 defensin-like genes in arabidopsis
Genome organization of more than 300 defensin-like genes in arabidopsis
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DOI：
10.1104/pp.105.060079
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发表时间：
2005-06-01
期刊：
影响因子：
7.4
通讯作者：
VandenBosch, KA
中科院分区：
文献类型：
--
作者：
Silverstein, KAT;Graham, MA;VandenBosch, KA
防御素是哺乳动物、昆虫和植物中一组古老且多样的小分子、富含半胱氨酸的抗菌肽。据已发表的报道，大多数物种的基因组含有15到50种防御素。从模式豆科植物蒺藜苜蓿的一组主要在根瘤中特异表达的类防御素序列（DEFLs）出发，我们构建了基序模型来搜索近乎完整的拟南芥（Arabidopsis thaliana）基因组。我们鉴定出317个DEFLs，但其中80%在拟南芥信息资源库中没有注释，且之前没有表达的证据。我们证明许多这些DEFL基因在拟南芥基因组中是成簇的，并且各个簇是由连续几轮的基因复制以及分化选择或纯化选择进化而来的。对来自五个DEFL簇的逆转录 - PCR产物进行测序，证实了我们的基因预测并验证了表达。对于四个最大的DEFL簇，我们提供了表达的首个证据，且最常在花组织中表达。为了确定其他植物家族中DEFLs的丰富程度，我们使用我们的基序模型搜索基因组研究所的基因索引，并鉴定出大约1100个DEFLs。这些表达的DEFLs大多在生殖组织中被发现，这与我们的逆转录 - PCR结果一致。对所有已鉴定的DEFLs基于序列的聚类揭示了不同的组织特异性或分类群特异性亚组。此前，我们及其他研究人员表明，超过300个DEFL基因在蒺藜苜蓿根瘤中表达，而根瘤是大多数植物所没有的器官。我们利用这些信息对拟南芥基因组进行注释，现在提供了在所有已测序植物的表达组织中存在一个大型DEFL超家族的证据。
Defensins represent an ancient and diverse set of small, cysteine- rich, antimicrobial peptides in mammals, insects, and plants. According to published accounts, most species' genomes contain 15 to 50 defensins. Starting with a set of largely nodule-specific defensin-like sequences ( DEFLs) from the model legume Medicago truncatula, we built motif models to search the near-complete Arabidopsis ( Arabidopsis thaliana) genome. We identified 317 DEFLs, yet 80% were unannotated at The Arabidopsis Information Resource and had no prior evidence of expression. We demonstrate that many of these DEFL genes are clustered in the Arabidopsis genome and that individual clusters have evolved from successive rounds of gene duplication and divergent or purifying selection. Sequencing reverse transcription- PCR products from five DEFL clusters confirmed our gene predictions and verified expression. For four of the largest clusters of DEFLs, we present the first evidence of expression, most frequently in floral tissues. To determine the abundance of DEFLs in other plant families, we used our motif models to search The Institute for Genomic Research's gene indices and identified approximately 1,100 DEFLs. These expressed DEFLs were found mostly in reproductive tissues, consistent with our reverse transcription- PCR results. Sequence- based clustering of all identified DEFLs revealed separate tissue- or taxon- specific subgroups. Previously, we and others showed that more than 300 DEFL genes were expressed in M. truncatula nodules, organs not present in most plants. We have used this information to annotate the Arabidopsis genome and now provide evidence of a large DEFL superfamily present in expressed tissues of all sequenced plants.