Gramaje David, Berlanas Carmen, Martínez-Diz María Del Pilar, Diaz-Losada Emilia, Antonielli Livio, Beier Sabrina, Gorfer Markus, Schmoll Monika, Compant Stéphane
Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja, Ctra. LO-20 Salida 13, 26007 Logroño, Spain.
Estación de Viticultura e Enoloxía de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n, 32427 Ourense, Spain.
J Fungi (Basel). 2020 Oct 29;6(4):255. doi: 10.3390/jof6040255.
The soil-borne fungus is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in , that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.
这种土传真菌是欧洲黑脚病最常见的致病因子。然而，对于这种真菌如何引发植物症状，人们还缺乏了解。在本研究中，我们对从无症状葡萄藤、杂草和土壤中分离出的三个菌株的基因组进行了测序、注释和分析。将测序得到的基因组与包括根和地上部病原体、白腐降解菌、室内生物劣化剂、腐生菌、暗隔内生菌和菌根在内的27种真菌物种的基因组进行了进一步比较。该菌株的基因组大小在64至65兆碱基对之间，每个菌株预测基因多达18548个。平均核苷酸同一性（ANI）表明，根据基因组内容，菌株存在差异。对直系同源基因簇进行了比较，在所有该菌株中特别检测到了与坏死相关的基因簇（坏死诱导肽和蛋白质以及乙烯诱导肽），以及一些与葡萄栽培中常用的杀菌剂（如铜）抗性相关的基因。有趣的是，在每个该菌株中检测到大量与碳水化合物活性酶相关的基因扩增，尤其是那些与糖苷水解酶相关的基因，这些基因可能参与植物组织的穿透或致病性。参与碳水化合物活性酶家族AA9和AA3 - 1的候选基因数量增加，支持了该菌株有效降解植物材料的能力。对与分泌组和小分泌蛋白相关的该基因的大量基因进行了进一步表征。此外，检测到存在几个基因簇，如通常在与真菌致病性相关的中发现的藤仓菌素样基因。所研究的三个菌株的表型在光反应方面进一步表现出差异。我们发现该菌株中编码光感受器的基因数量增加，并且我们展示了序列改变。总之，结果突出了该菌株中存在的几个基因簇，这些基因簇可能与内生生活方式、致病性、植物浸软和植物组织降解以及对金属和类金属污染土壤的适应性和光反应有关。
