Laboratory of Phytopathology, Wageningen University, 6708PB, Wageningen, the Netherlands.
Department of Biology, Faculty of Sciences, University of A Coruña, A Coruña, Spain.
BMC Genomics. 2019 Mar 12;20(1):203. doi: 10.1186/s12864-019-5580-x.
Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae.
Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed.
Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.
葡萄孢属（目前包含约 35 个种）的真菌能够感染超过 1400 种不同的植物物种，并在广泛的经济重要作物中造成损失。研究得最好的物种是灰葡萄孢，它的寄主范围很广，是研究最深入的一种坏死性植物病原真菌。大多数其他葡萄孢属的物种寄主范围较窄，研究得较少。为了描述不同葡萄孢属代表种之间的基因组变异，我们对 9 种葡萄孢属的物种进行了测序和注释：葡萄孢、卷枝毛霉、椭圆毛霉、甘蓝根肿菌、风信子葡萄孢、水仙葡萄孢、芍药葡萄孢、大葱葡萄孢和郁金香葡萄孢。
生物信息学和比较基因组学工具被用来确定所有葡萄孢属物种中共有 7668 个蛋白家族的核心，这些蛋白家族将它们分为两个不同的系统发育分支。所有 9 种葡萄孢属的物种的分泌组在数量上相似（预测蛋白数量在 716 到 784 个之间）。对分泌组的分子功能的详细分析表明，共享的活性非常相似。在灰葡萄孢中功能研究过的效应子的同源物也存在于其他葡萄孢属物种中。观察到次生代谢物生物合成关键酶的存在/缺失的复杂模式。
葡萄孢的比较基因组学表明，总体而言，物种在分泌蛋白和已知效应子中共享主要特征和蛋白家族。我们的研究为研究葡萄孢属的寄主范围决定因素提供了线索，并为阐明这些物种感染过程中效应子候选物的作用提供了一个起点。
