Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum
Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum
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DOI：
10.1093/gbe/evz087
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发表时间：
2019-04
影响因子：
3.3
通讯作者：
A. Tsushima;P. Gan;Naoyoshi Kumakura;M. Narusaka;Y. Takano;Y. Narusaka;K. Shirasu
中科院分区：
文献类型：
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作者：
A. Tsushima;P. Gan;Naoyoshi Kumakura;M. Narusaka;Y. Takano;Y. Narusaka;K. Shirasu
摘要植物病原体基因组处于不断变化的压力之下，因为病原体与其宿主锁定在进化的军备竞赛中，其中病原体进化效应基因以操纵其宿主，而宿主进化免疫组分以识别这些基因的产物。刺盘孢（Colletotrichum higginsianum，Ch）是一种侵染拟南芥（Arabidopsis thaliana）等兰科植物的真菌病原菌。以往的研究表明，Ch对不同的拟南芥生态型的毒力不同，表明存在共同进化的选择压力。然而，菌株间的基因组变异在Ch还没有被研究。在这里，我们测序和组装Ch菌株的基因组，导致高度连续的基因组组装，将其与另一菌株的染色体水平基因组组装进行比较，以确定菌株之间的基因组变异。我们发现，这两个密切相关的菌株在大规模的重排，菌株特异性区域的存在，和效应候选基因集，这些变化往往与转座因子（TE）。Ch具有由具有更多效应子候选基因的基因稀疏、TE密集区域和具有保守基因的基因密集、TE稀疏区域组成的区室化基因组。此外，效应候选基因的保守模式和同线区域的分析表明，这两个菌株在其效应候选基因集的变化，因为从头进化，水平基因转移，或基因丢失后的分歧。我们的研究结果揭示了在这种无性病原体中产生基因组多样性的机制，这对于理解其对宿主的适应是很重要的。
Abstract Phytopathogen genomes are under constant pressure to change, as pathogens are locked in an evolutionary arms race with their hosts, where pathogens evolve effector genes to manipulate their hosts, whereas the hosts evolve immune components to recognize the products of these genes. Colletotrichum higginsianum (Ch), a fungal pathogen with no known sexual morph, infects Brassicaceae plants including Arabidopsis thaliana. Previous studies revealed that Ch differs in its virulence toward various Arabidopsis thaliana ecotypes, indicating the existence of coevolutionary selective pressures. However, between-strain genomic variations in Ch have not been studied. Here, we sequenced and assembled the genome of a Ch strain, resulting in a highly contiguous genome assembly, which was compared with the chromosome-level genome assembly of another strain to identify genomic variations between strains. We found that the two closely related strains vary in terms of large-scale rearrangements, the existence of strain-specific regions, and effector candidate gene sets and that these variations are frequently associated with transposable elements (TEs). Ch has a compartmentalized genome consisting of gene-sparse, TE-dense regions with more effector candidate genes and gene-dense, TE-sparse regions harboring conserved genes. Additionally, analysis of the conservation patterns and syntenic regions of effector candidate genes indicated that the two strains vary in their effector candidate gene sets because of de novo evolution, horizontal gene transfer, or gene loss after divergence. Our results reveal mechanisms for generating genomic diversity in this asexual pathogen, which are important for understanding its adaption to hosts.