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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #399466

Research Project: Improving Fruit Crop Traits Through Advanced Genomic, Breeding, and Management Technologies

Location: Innovative Fruit Production, Improvement, and Protection

Title: Improved genome assembly resource of the plant pathogen Fusarium avenaceum

item Gottschalk, Christopher
item Evans, Breyn
item Collum, Tamara - Tami

Submitted to: American Phytopathological Society
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2022
Publication Date: 3/28/2023
Citation: Gottschalk, C.C., Evans, B.E., Collum, T.D. 2023. Improved genome assembly resource of the plant pathogen Fusarium avenaceum. American Phytopathological Society.

Interpretive Summary: Fusarium avenaceum is a generalist fungus that can infect many different crops and is a concern for food safety due to its ability to produce toxins. Genome sequences are valuable resources to study fungal biology including the genes involved in the crop infection pathway and genes involved in the production of toxins. Currently, there are 12 available genomes for Fusarium avenaceum. However, all of them were produced using short-read sequencing resulting in fragmented and incomplete genomes sequences. Here, we present a new genome assembly for Fusarium avenaceum that is of higher quality than all other previously released genomes. We accomplished this by using the lastest long-read sequencing technology to assemble a genome sequence that matches the expected chromosome number and thoroughly annotate the genes. Our annotation also included an analysis of the gene clusters that are associated with toxin and other biochemical production pathways. This genomic resource will facilitate further research on plant pathology, food safety, and Fusarium sp. diversity.

Technical Abstract: Fusarium avenaceum is a generalist plant pathogen of concern due to its potential to produce mycotoxins on plant products. Previous research efforts have sequenced and assembled genomes of F. avenaceum. However, those works relied on limited next-generation sequencing technologies that resulted in fragmented and incomplete genome assemblies. To address this, we utilized high-depth 3rd generation long-read sequencing and several different genome assembly software to generate a new, highly contiguous genome of F. avenaceum. Moreover, we conducted a thorough annotation of the genome using a mix of long-read cDNA and short-read RNAseq data. Our genome was more contiguous than the current reference genome Fustri1, matched the estimated genome size and chromosome number, and contained a similar number of annotated genes to other F. avenaceum genome assemblies. Lastly, we conducted a secondary metabolite (SM) cluster analysis that identified 60 gene clusters associated with SM biosynthesis, five more than the reference F. avenaceum genome. In conclusion, our genome and associated annotation information will help advance research on plant-fungal interactions, food safety, and Fusarium sp. diversity.