Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA.
Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37831, USA.
G3 (Bethesda). 2021 Apr 15;11(4). doi: 10.1093/g3journal/jkab071.
Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.
Neonectria faginata 和 Neonectria coccinea 是一种被称为山毛榉树皮病（BBD）的昆虫-真菌疾病复合体的病原体，已知其会导致北美和欧洲山毛榉林分死亡。这两个真菌物种一直是广泛的生态和疾病管理研究的焦点，但在为微观和宏观进化研究生成基因组资源方面进展较少。在这里，我们分别报告了 N. faginata 和 N. coccinea 的 42.1 和 42.7 Mb 高度连续基因组组装，这些组装是使用 Illumina 技术获得的。这两个物种的基因数量计数（12,941 和 12,991）和具有功能类别分配的预测基因百分比（64 和 65%）非常相似。这两个物种的预测蛋白质组中约有 32%与致病性相关的蛋白质同源，但 N. coccinea 显示出更多的预测丝裂原活化蛋白激酶基因，这些基因可能是导致 N. faginata 和 N. coccinea 之间疾病严重程度差异的毒力决定因素。还发现了大量编码能够降解复杂植物多糖的碳水化合物活性酶的基因，以及少量预测的分泌效应蛋白、次生代谢物生物合成簇和细胞色素氧化酶 P450 基因。这些酶和效应蛋白的组合与这两种真菌病原体的半活体生物生活方式相关，并反映了这种生活方式。系统基因组分析和时树估计表明，N. faginata 和 N. coccinea 物种的分化可能发生在约 410 万年前。在注释的线粒体基因组中也观察到了差异，因为它们的大小分别为 81.7 kb（N. faginata）和 43.2 kb（N. coccinea）。在 N. faginata 中观察到的线粒体 DNA 扩张归因于内含子入侵不同的内含子和基因间位置。N. faginata 和 N. coccinea 的这两个初始草图基因组为增加我们对这两个 nectriaceous 植物病原物种的基本遗传学、进化机制和分子生理学的理解提供了有价值的工具。
