Comparative genome analyses suggests a hemibiotrophic lifestyle and virulence dfferences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea

Authors: Salgado-Salazar, Catalina; SKALTSAS, DEMETRA - Orise Fellow; Phipps, Tunesha; Castlebury, Lisa

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2021
Publication Date: 3/9/2021
Citation: Salgado-Salazar, C., Skaltsas, D.N., Phipps, T., Castlebury, L.A. 2021. Comparative genome analyses suggests a hemibiotrophic lifestyle and virulence dfferences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea. G3, Genes/Genomes/Genetics. 11(4):jkab071. https://doi.org/10.1093/g3journal/jkab071.
DOI: https://doi.org/10.1093/g3journal/jkab071

Interpretive Summary: The genus Neonectria (family Nectriaceae) harbors a variety of widespread and destructive fungal plant pathogens. Pathogenic species in this genus affect a variety of crops including forest, timber productions, and fruit trees in North America and Europe. However, relatively few completed genomes have been generated and analyzed for these pathogens. This study generated and analyzed high quality genome sequences for Neonectria faginata and N. coccinea, both of which cause beech bark disease and characterized the genes that were discovered. These are the first genomes to be completed for these two pathogenic species. This research will be useful for mycologists and plant pathologists to develop quick and efficient assays for its targeted detection, to understand pathogenicity and to develop strategies to control the spread and prevent the economic and societal losses associated with beech bark disease.

Technical Abstract: Neonectria faginata and N. 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 towards 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 – 12,991) and percentages of predicted genes with assigned functional categories (64 – 65%). Approximately 4.9 to 7.1% of the genomes consist of transposable elements (TE) indicating they have little effect on genome expansion. However, a detailed analysis of the TE content in N. coccinea revealed a higher ratio of Class I to Class II elements mostly attributable to variation in gene copy number. Close to 32% of the predicted proteomes are homologous to proteins involved in pathogenicity, and also include 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 (CYP) genes. This arsenal of enzymes and effectors correlates with and reflects the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and time-tree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ~4.1 Million years ago (Mya). Differences were 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 apparently attributable 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.