Fusarium graminearum PH-1 Genome sequencing. Fusarium graminearum PH-1

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. Here we refined the reference genome sequences of Fusarium graminearum by using PacBio SMRT long-read sequencing and Illumina short read sequencing. We generated 13 Gb (>300x) high-quality long-reads for a YL (Yangling) lab stock of F. graminearum PH-1 with PacBio Sequel platform and assembled them into 10 contigs de novo. By comparing the PacBio assembly with the most recent public assembly RR1 (Ensembl Fungi) of PH-1, a total of 315 different regions/sites were identified. To determine which assembly is correct at these regions/sites, we re-sequenced the YL lab stock and additional two lab stocks of PH-1 ZJU (Zhejiang University) and MSU (Michigan State University) by Illumina and obtained >90x high-quality short reads for each lab stock. The Illumina short-reads of the three PH-1 lab stocks and PacBio long-reads were aligned to the two genome assemblies, respectively. Based on the alignments, 7 mis-assembly regions caused by repeat sequences, 200 base errors, and 42 InDel errors in the RR1 assembly, which impacts the annotation of 74 protein-coding genes, were evidenced by at least two PH-1 lab stocks. We corrected all the errors in the RR1 assembly and generated an updated version (named YL1) of reference genome sequences of Fusarium graminearum PH-1.