Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
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DOI：
10.1371/journal.ppat.1003037
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发表时间：
2012
期刊：
影响因子：
6.7
通讯作者：
Grigoriev IV
中科院分区：
文献类型：
--
作者：
Ohm RA;Feau N;Henrissat B;Schoch CL;Horwitz BA;Barry KW;Condon BJ;Copeland AC;Dhillon B;Glaser F;Hesse CN;Kosti I;LaButti K;Lindquist EA;Lucas S;Salamov AA;Bradshaw RE;Ciuffetti L;Hamelin RC;Kema GH;Lawrence C;Scott JA;Spatafora JW;Turgeon BG;de Wit PJ;Zhong S;Goodwin SB;Grigoriev IV
Dothideomycetes纲是最大的真菌类群之一，具有高水平的生态多样性，包括许多植物病原体，感染广泛的宿主。在这里，我们比较了这类18个成员的基因组特征，包括6个necrotrophs，9个（半）biotrophs和3个saprotrophs，以分析基因组结构，进化和致病的不同策略。Dothideomycetes很可能是从2.8亿年前的共同祖先进化而来的。18个基因组序列由于重复内容的变化而在大小上显著不同，但在（核心）基因的数量上显示出小得多的变化。在现存的基因组中，基因顺序似乎主要是在染色体边界内通过多重倒位进行重排的，这些基因组经常由相邻的简单重复序列划分。几种盾壳菌含有一个或多个基因贫乏，转座因子（TE）丰富的puericum染色体的未知功能。这18种盾壳菌提供了一个广泛的基因目录，涉及纤维素降解，蛋白水解，次生代谢和富含半胱氨酸的小分泌蛋白。在Dothideomycetes中的两个主要植物病原体目的祖先，Capnodiales和Pleosporales，可能具有不同的致病模式，前者比后者具有更少的这些基因。这些基因中的许多基因在转座因子附近富集，这表明由于重复诱导点突变（RIP）的影响，进化更快。包括氧化还原酶在内的同线基因组在大多数盾壳菌中是保守的，并在L. maculans，表明可能的功能，在应对氧化应激。 Dothideomycetes是最大和最具生态多样性的真菌类别，包括许多具有高经济影响的植物病原体。目前有18个Dothideomycetes的基因组序列，其中14个是本文和几篇配套论文中新描述的，在比较分析中允许前所未有的分辨率。这18种生物具有不同的生活方式和植物致病策略。其中三种仅以死亡的有机物为食，六种是坏死营养型（杀死宿主植物细胞），一种是活体营养型（与宿主植物细胞的活细胞形成联系并因此以其为食），八种是半活体营养型（具有初始活体营养阶段，并在后期杀死宿主植物）。这些不同的生活方式也反映在每个群体中存在的基因组中。例如，参与碳水化合物降解和次级代谢的基因组在坏死营养生物中扩增。许多参与发病机制的基因位于重复序列附近，这被认为加速了它们的进化。鉴定了具有保守基因顺序的基因块。除此之外，我们推断，中同线的机制，一种类型的基因组进化特有的Dothideomycetes，是通过染色体内倒位。
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress. Dothideomycetes is the largest and most ecologically diverse class of fungi that includes many plant pathogens with high economic impact. Currently 18 genome sequences of Dothideomycetes are available, 14 of which are newly described in this paper and in several companion papers, allowing unprecedented resolution in comparative analyses. These 18 organisms have diverse lifestyles and strategies of plant pathogenesis. Three feed on dead organic matter only, six are necrotrophs (killing the host plant cells), one is a biotroph (forming an association with and thus feeding on the living cells of the host plant cells) and 8 are hemibiotrophs (having an initial biotrophic stage, and killing the host plant at a later stage). These various lifestyles are also reflected in the gene sets present in each group. For example, sets of genes involved in carbohydrate degradation and secondary metabolism are expanded in necrotrophs. Many genes involved in pathogenesis are located near repetitive sequences, which are believed to speed up their evolution. Blocks of genes with conserved gene order were identified. In addition to this we deduce that the mechanism for mesosynteny, a type of genome evolution particular to Dothideomycetes, is by intra-chromosomal inversions.
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