Data from: Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi

Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease-causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of C. orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray.Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate-degrading enzymes. Many SSP and secondary metabolite synthesis genes were up-regulated during initial stages of host colonization, while the necrotrophic stage of growth is characterized by up-regulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage-specific gene expression profiles of expanded classes of potential pathogenicity genes.半活体营养型植物病原真菌（Hemibiotrophic fungal plant pathogens）是一类在农业生产中具有重要意义的致病病原物，其先在宿主活组织上营共生生长，后续转为死体营养阶段导致宿主组织坏死死亡。该类群中，炭疽菌属（Colletotrichum）物种是众多作物的毁灭性病原。鉴定植物病原炭疽菌基因组中扩增的基因家族（尤其是与半活体营养特定阶段相关的基因家族），有助于解析此类病原侵染多种宿主的分子机制。本研究对侵染葫芦科植物与本氏烟（Nicotiana benthamiana）的瓜类炭疽菌（Colletotrichum orbiculare），以及可侵染多种作物的胶孢炭疽菌（Colletotrichum gloeosporioides）的基因组进行了测序与分析，重点关注潜在致病相关的基因组特征。同时，利用定制化微阵列（microarray）分析了瓜类炭疽菌侵染本氏烟过程中的基因表达调控模式。相较于其他真菌，两个基因组中均存在扩增的基因家族，包括编码小型分泌蛋白（small secreted proteins, SSPs）的序列、次生代谢产物合成基因、蛋白酶以及碳水化合物降解酶类。多数SSP与次生代谢产物合成基因在宿主定殖初始阶段呈上调表达，而死体营养生长阶段则以降解酶编码序列的上调表达为典型特征。瓜类炭疽菌的半活体营养过程，以扩增的潜在致病基因家族呈现显著的阶段特异性表达谱为核心特征。