Institute of Sciences of Food Production, National Research Council, Bari, Italy.
BMC Genomics. 2018 Sep 11;19(1):662. doi: 10.1186/s12864-018-5049-3.
So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus Trichoderma, the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions. Here we present the genome of a biocontrol strain formerly known as Trichoderma harzianum ITEM 908, which exhibits both growth promoting capabilities and antagonism against different fungal pathogens, including Fusarium graminearum, Rhizoctonia solani, and the root-knot nematode Meloidogyne incognita. By genomic analysis of ITEM 908 we investigated the occurrence and the relevance of genes associated to biocontrol and stress tolerance, providing a basis for future investigation aiming to unravel the complex relationships between genomic endowment and exhibited activities of this strain.
The MLST analysis of ITS-TEF1 concatenated datasets reclassified ITEM 908 as T. atrobrunneum, a species recently described within the T. harzianum species complex and phylogenetically close to T. afroharzianum and T. guizhouense. Genomic analysis revealed the presence of a broad range of genes encoding for carbohydrate active enzymes (CAZYmes), proteins involved in secondary metabolites production, peptaboils, epidithiodioxopiperazines and siderophores potentially involved in parasitism, saprophytic degradation as well as in biocontrol and antagonistic activities. This abundance is comparable to other Trichoderma spp. in the T. harzianum species complex, but broader than in other biocontrol species and in the species T. reesei, known for its industrial application in cellulase production. Comparative analysis also demonstrated similar genomic organization of major secondary metabolites clusters, as in other Trichoderma species.
Reported data provide a contribution to a deeper understanding of the mode of action and identification of activity-specific genetic markers useful for selection and improvement of biocontrol strains. This work will also enlarge the availability of genomic data to perform comparative studies with the aim to correlate phenotypic differences with genetic diversity of Trichoderma species.
到目前为止，生物防治剂的选择主要是通过耗时的体外对抗试验，然后在温室和田间进行广泛的试验。一种替代方法是应用高通量技术，该技术允许对菌株进行广泛的筛选和比较，以获得所需的遗传特性。在木霉属中，根据最近的分类修订，需要重新考虑将特定特征或菌株分配给一个物种的过去做法。在这里，我们介绍了一种以前被称为哈茨木霉 ITEM 908 的生物防治菌株的基因组，该菌株表现出促进生长和拮抗不同真菌病原体的能力，包括禾谷镰刀菌、立枯丝核菌和根结线虫。通过对 ITEM 908 的基因组分析，我们研究了与生物防治和应激耐受相关的基因的发生和相关性，为未来的研究提供了基础，旨在揭示该菌株的基因组赋存与表现出的活性之间的复杂关系。
ITS-TEF1 串联数据集的 MLST 分析将 ITEM 908 重新归类为 T.atrobrunneum，这是一个最近在哈茨木霉种复合体中描述的物种，与 T.afroharzianum 和 T.guizhouense 亲缘关系较近。基因组分析显示，存在广泛的基因编码碳水化合物活性酶（CAZYmes）、参与次生代谢产物生产的蛋白质、肽类、二硫二氧杂环戊烷和铁载体，这些基因可能参与寄生、腐生降解以及生物防治和拮抗活性。这种丰富度与哈茨木霉种复合体中的其他木霉属物种相当，但比其他生物防治物种和以纤维素酶生产而闻名的工业应用物种 T.reesei 更广泛。比较分析还表明，主要次生代谢物簇的基因组组织与其他木霉属物种相似。
报告的数据有助于更深入地了解作用模式，并确定用于选择和改进生物防治菌株的特定活性的遗传标记。这项工作还将扩大基因组数据的可用性，以便与木霉属物种的表型差异与遗传多样性进行比较研究。
