454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction
454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction
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DOI：
10.1111/j.1364-3703.2011.00723.x
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发表时间：
2012-01-01
影响因子：
4.9
通讯作者：
Duplessis, Sebastien
中科院分区：
文献类型：
--
作者：
Fernandez, Diana;Tisserant, Emilie;Duplessis, Sebastien
咖啡（Coffea arabica L.）是热带和亚热带国家的主要出口和经济作物之一，因锈菌Hemileia badatrix而遭受严重损失。在与咖啡相容的相互作用过程中对 H. badatrix 的转录组进行了分析，以获得感染期间表达的基因的详尽库并鉴定潜在的效应基因。对从 21 天感染锈病的叶子中获得的混合咖啡和锈病 cDNA 进行大规模测序 (454-GS-FLEX Titanium)，生成了 352 146 个序列，这些序列组装成 22 774 个重叠群。在缺乏咖啡或半月莲的任何参考基因组序列的情况下，使用表达序列标签（EST）内的特定三核苷酸频率以及针对一组双子叶植物和担子菌基因组的母细胞同源性来区分病原体和植物序列。大约 30% (6763) 的重叠群被分配给 H. badatrix，61% (13 951) 被分配给 C. arabica。大多数（60%）锈病序列与任何基因组数据库都没有显示出同源性，表明它们是潜在的新型真菌基因。对 6763 个 H.vastatrix 重叠群的计算机分析预测了 382 个分泌蛋白，并鉴定了亚麻锈病吸器表达分泌蛋白 (HESP) 和豆锈病转移蛋白 1 (RTP1) 的同源物。这些锈病候选效应子显示出保守的氨基酸结构域和半胱氨酸位置的保守模式，表明宿主植物感染期间的保守功能。对选定锈病基因的定量逆转录聚合酶链反应分析揭示了咖啡叶感染过程中的动态表达模式。这项研究为农业上重要的植物病原体 H.vastatrix 提供了第一个有价值的基因组资源和第一个全面的阿拉比卡 EST 数据集。
Coffee (Coffea arabica L.), one of the key export and cash crops in tropical and subtropical countries, suffers severe losses from the rust fungus Hemileia vastatrix. The transcriptome of H. vastatrix was analysed during a compatible interaction with coffee to obtain an exhaustive repertoire of the genes expressed during infection and to identify potential effector genes. Large-scale sequencing (454-GS-FLEX Titanium) of mixed coffee and rust cDNAs obtained from 21-day rust-infected leaves generated 352 146 sequences which assembled into 22 774 contigs. In the absence of any reference genomic sequences for Coffea or Hemileia, specific trinucleotide frequencies within expressed sequence tags (ESTs) and blast homology against a set of dicots and basidiomycete genomes were used to distinguish pathogen from plant sequences. About 30% (6763) of the contigs were assigned to H. vastatrix and 61% (13 951) to C. arabica. The majority (60%) of the rust sequences did not show homology to any genomic database, indicating that they were potential novel fungal genes. In silico analyses of the 6763 H. vastatrix contigs predicted 382 secreted proteins and identified homologues of the flax rust haustorially expressed secreted proteins (HESPs) and bean rust transferred protein 1 (RTP1). These rust candidate effectors showed conserved amino-acid domains and conserved patterns of cysteine positions suggestive of conserved functions during infection of host plants. Quantitative reverse transcription-polymerase chain reaction profiling of selected rust genes revealed dynamic expression patterns during the time course of infection of coffee leaves. This study provides the first valuable genomic resource for the agriculturally important plant pathogen H. vastatrix and the first comprehensive C. arabica EST dataset.