Table_8_Genome-Wide Signatures of Selection in Colletotrichum kahawae Reveal Candidate Genes Potentially Involved in Pathogenicity and Aggressiveness.XLS

Plants and their pathogens are engaged in continuous evolutionary battles, with pathogens evolving to circumvent plant defense mechanisms and plants responding through enhanced protection to prevent or mitigate damage induced by pathogen attack. Managed ecosystems are composed of genetically identical populations of crop plants with few changes from year to year. These environments are highly conducive to the emergence and dissemination of pathogens and they exert selective pressure for both qualitative virulence factors responsible for fungal pathogenicity, and quantitative traits linked to pathogen fitness, such as aggressiveness. In this study, we used a comparative genome-wide approach to investigate the genomic basis underlying the pathogenicity and aggressiveness of the fungal coffee pathogen Colletotrichum kahawae infecting green coffee berries. The pathogenicity was investigated by comparing genomic variation between C. kahawae and its non-pathogenic sibling species, while the aggressiveness was studied by a genome-wide association approach with groups of isolates with different phenotypic profiles. High genetic differentiation was observed between C. kahawae and the most closely related species with 5,560 diagnostic SNPs identified, in which a significant enrichment of non-synonymous mutations was detected. Functional annotation of these non-synonymous mutations revealed a significant enrichment mainly in two gene ontology categories, “oxidation–reduction process” and “integral component of membrane.” Finally, the annotation of several genes potentially under-selection revealed that C. kahawae’s pathogenicity may be a complex biological process, in which important biological functions, such as, detoxification and transport, regulation of host and pathogen gene expression, and signaling are involved. On the other hand, the genome-wide association analyses for aggressiveness were able to identify 10 SNPs and 15 SNPs of small effect in single and multi-association analysis, respectively, from which 7 were common, giving in total 18 SNPs potentially associated. The annotation of these genomic regions allowed the identification of four candidate genes encoding F-box domain-containing, nitrosoguanidine resistance, Fungal specific transcription factor domain-containing and C6 transcription factor that could be associated with aggressiveness. This study shed light, for the first time, on the genetic mechanisms of C. kahawae host specialization.

植物与其病原体持续进行着一场演化之战，病原体通过演化来规避植物的防御机制，而植物则通过增强的保护能力来抵御或减轻病原体攻击造成的损害。管理型生态系统由基因型完全相同的作物种群组成，年复一年变化甚微。这些环境极为有利于病原体的出现和传播，并对具有真菌致病性的定性毒力因子以及与病原体适应性相关的定量性状，如攻击性，施加了选择压力。在本研究中，我们采用比较基因组学方法，探究了真菌咖啡病原体Colletotrichum kahawae感染绿色咖啡豆的致病性和攻击性的基因组基础。通过比较C. kahawae与其非致病性同属种之间的基因组变异来研究致病性，而通过全基因组关联分析方法研究具有不同表型特征分离株组的攻击性。观察到C. kahawae与其最接近的物种之间存在高度遗传分化，共识别出5,560个诊断性单核苷酸多态性（SNPs），其中检测到非同义突变显著富集。这些非同义突变的机能注释揭示了主要富集在两个基因本体学类别中，即“氧化还原过程”和“膜组成成分”。最后，对可能未充分选择的几个基因的注释表明，C. kahawae的致病性可能是一个复杂的生物学过程，其中涉及重要的生物学功能，如解毒和运输、宿主和病原体基因表达的调控以及信号传导。另一方面，针对攻击性的全基因组关联分析在单关联和多关联分析中分别识别出10个SNPs和15个具有小效应的SNPs，其中7个是共同的，总共18个SNPs可能与攻击性相关。这些基因组区域的注释允许鉴定出四种候选基因，它们分别编码含有F-box结构域、硝基胍耐药性、真菌特异性转录因子结构域和C6转录因子的蛋白质，这些蛋白质可能与攻击性相关。本研究首次揭示了C. kahawae宿主特化的遗传机制。