The filamentous ascomycete fungus Fusarium graminearum is the predominant causal agent of Fusarium head blight (FHB), one of the most devastating diseases on cereal crops worldwide. In addition to FHB, F. graminearum causes other diseases in cereals during their life cycle including crown rot, root rot, and seedling blight. Given its scientific/economic importance, F. graminearum has been listed as one of the top 10 most important fungal pathogens, ranking the fourth. F. graminearum is homothallic and produces abundant perithecia relatively synchronously under laboratory conditions, making it an ideal system for studying sexual development. The relatively high rate of homologous recombination and ability to easily obtain homokaryotic transformants have made molecular studies in F. graminearum efficient and productive.

       The reference genome of F. graminearum PH-1 comprising four chromosomes and a mitochondrial genome was originally sequenced by Sanger sequencing (Cuomo et al., 2007) and completed with Illumina resequencing data (King et al., 2015; King et al., 2017). The gene model annotation has been improved by multiple revisions (Cuomo et al., 2007; Wong et al., 2011; King et al., 2015; King et al., 2017). Although previous annotation was generated by integrating multiple gene prediction algorithms, most gene models contain only coding sequences, missing 5’- and/or 3’-untranslated regions. No splice isoform information is available. Functional genomic studies rely on accurate gene and transcript annotation.

       Here, we refined the most recent public genome assembly of PH-1 (RR1, Ensembl Fungi) with PacBio SMRT long-read sequencing and corrected 7 mis-assemblies, 200 base errors, and 42 InDel errors. We generated a comprehensive transcript annotation (named YL1) comprising 51,617 isoforms from 17,189 genes for PH-1 with PacBio Iso-Seq and strand-specific RNA-Seq of multiple tissues. Compared to the previous annotation (RR1) consisting of only 14,145 transcripts from 14,145 genes, the updated reference annotation YL1 is much more comprehensive and complete. To facilitate its usage, we created the FgBase (fgbase.wheatscab.com), a Fusarium graminearum genome database that allows users to browse, search, and download the updated genome and annotation.

References

1.Cuomo CA, Guldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, Walton JD, Ma LJ, Baker SE, Rep M, et al. 2007. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317(5843): 1400-1402.

2.King R, Urban M, Hammond-Kosack KE. 2017. Annotation of Fusarium graminearum (PH-1) Version 5.0. Genome Announc 5(2).

3.King R, Urban M, Hammond-Kosack MC, Hassani-Pak K, Hammond-Kosack KE. 2015. The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum. BMC Genomics 16: 544.

4.Wong P, Walter M, Lee W, Mannhaupt G, Munsterkotter M, Mewes HW, Adam G, Guldener U. 2011. FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. Nucleic Acids Res 39(Database issue): D637-639.