Draft Genome Sequence of Fusarium fujikuroi B14, the Causal Agent of the Bakanae Disease of Rice

Abstract

Here, we present the genome sequence of a Korean strain (B14) of Fusarium fujikuroi, a fungal rice pathogen. The final assembly consists of 455 contigs with 43,810,516 bp and 14,017 predicted genes. Comparison with the F. verticillioides 7600 genome revealed a reference coverage of 83% (66.3% of reads mapped).

GENOME ANNOUNCEMENT

The genus Fusarium, a large group of filamentous ascomycetous fungi, includes a broad range of plant pathogens in many agricultural crops worldwide (1). Some species produce mycotoxins harmful to both humans and plants (2). Thus far, genomes of three species (F. graminearum, F. oxysporum, and F. verticillioides) have been sequenced (3–5). F. fujikuroi (teleomorph, Gibberella fujikuroi; synonym, G. fujikuroi mating population C) is a biologically and phylogenetically distinct species within the G. fujikuroi species complex and causes bakanae disease of rice (1, 6). This fungus also produces several toxic secondary metabolites in infected plants (1). Here, we present the genome sequence of F. fujikuroi (strain B14) isolated from rice in South Korea and confirm its pathogenicity in rice. This is the first available F. fujikuroi whole-genome sequence and the second, after the F. verticillioides 7600 strain, among the G. fujikuroi complex.

Genome sequencing of F. fujikuroi B14 was carried out using an Illumina HiSeq 2000-based whole-genome shotgun strategy. A total of 35,306,706 paired-end reads of ~3.57 Gb (101 nucleotide [nt] cycle, 486-bp average paired distance) were preprocessed and de novo assembled using CLC Genomics workbench 5.5. Initially, the assembly was 43,794,120 bp in length with 338 scaffolds (N₅₀ 678,621 bp, 48.3% G+C, 1,079 contigs). After automatic gap closing using GapFiller version 1.9 (http://www.baseclear.com) with the same reads, the final assembly consisted of 455 contigs in 333 scaffolds with a length of 43,810,516 bp exclusive of N’s in remaining gaps. After masking repetitive sequences using a search against Repbase (http://www.girinst.org/repbase), 14,017 protein-coding genes were predicted using Augustus 2.5.5 (http://augustus.gobics.de) with F. graminearum parameters. Based on a BLASTP search against the UniRef90 database, significant matches (E value <10^–5) were identified for 13,734 genes; 9,143 hits were derived from F. oxysporum. We also identified 576 tRNA genes using tRNAscan-SE (7). For comparative genomic analysis, the preprocessed Illumina reads were mapped to chromosomal reference sequences for the three known Fusarium species (http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html). F. verticillioides 7600 was most similar to B14 in terms of reference coverage (83%; 66.3% of reads were mapped). The percent coverage values of F. oxysporum 4287 and F. graminearum PH-1 were 57% and 29%, respectively. BLASTP analysis showed that 46.2% and 42.1% of the B14 genes matched those of F. oyxsporum (total, 17,701 genes) and F. verticillioides (14,188 genes), respectively. In the B14 genome, all conserved gene clusters for secondary metabolites previously characterized in F. fujikuroi were identified, including those for gibberellin, fumonisin, bikaverin, melanin, fusarin, fusaric acid, and carotenoids. Additionally, F. fujikuroi B14, confirmed as the MAT1-2 mating type strain, carries 20 polyketide synthase (PKS) genes, including two nonreducing PKS and four PKS-NRPS (non-ribosomal peptide synthetase) hybrid genes.

In conclusion, the F. fujkuroi B14 genome will contribute to a greater understanding of the biology and evolution of the G. fujikuroi species complex, as well as the genus Fusarium.

Nucleotide sequence accession number.

The sequence determined in this study was deposited in the GenBank database under accession number ANFV00000000.