ABSTRACT
Here, we present the genome sequence of an isolate (14004) of Fusarium oxysporum f. sp. melongenae, an eggplant pathogen. The final assembly consists of 1,631 scaffolds with 53,986,354 bp (G+C content, 46.4%) and 16,485 predicted genes.
GENOME ANNOUNCEMENT
Fusarium species are some of the most important phytopathogenic and toxigenic fungi, causing various diseases on nearly every economically important plant species. Aside from their economic importance, species of Fusarium also serve as key model organisms for biological research (1).
Fusarium wilt of eggplant caused by Fusarium oxysporum f. sp. melongenae is an economically important soilborne disease limiting eggplant production worldwide. This pathogen was initially reported in Japan in 1958 (2), and the first report in China was in 2005 (3). Here, we report a draft assembly for F. oxysporum f. sp. melongenae isolate 14004, a field strain originally collected in Guangdong Province, China, where Fusarium wilt of eggplant was observed over 10 years ago and is currently endemic in the area.
The mycelium of fungal hyphae was grown on cellophane over potato dextrose agar (PDA), and 500 mg of mycelium was used for DNA extraction with the Qiagen DNeasy plant minikit (Qiagen, Mississauga, Canada); then, 1 μg of genomic DNA was sent for sequencing at Génome Québec (Montreal, Canada), specifying 100-bp paired-end reads with a 300-bp insert. Over 43 million paired-end reads totaling 10.7 Gb were received. The genome was assembled using the programs Velvet version 1.2.10 (4), ABySS version 2.0.1 (5), and SOAPdenovo version 2.04 (6), with odd-numbered kmers between 21 and 91. Assembly quality was assessed by examining the N50 value and by examining the total number of scaffolds produced by the programs. The initial assembly was 54,488,475 bp in length, with an N50 value of 568,281 bp, resulting in 4,617 scaffolds. After removing scaffolds that were smaller than 200 bp by using a perl script, the final assembly consisted of 1,631 scaffolds with a genome size of 53,986,354 bp (G+C content, 46.4%). A total of 16,485 protein-coding genes were predicted from the assembly, with the highest N50 (kmer = 77, ABySS) using AUGUSTUS version 3.2.2 (7) based on gene models from Fusarium oxysporum.
Accession number(s).
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. MPIL00000000. The version described in this paper is version MPIL01000000.
ACKNOWLEDGMENTS
This work was supported by the National Natural Science Foundation of China (grant 31301627) and Natural Science Foundation of Guangdong Province (grant S2012040006912).
Footnotes
Citation Dong Z, Hsiang T, Luo M, Xiang M. 2017. Draft genome sequence of an isolate of Fusarium oxysporum f. sp. melongenae, the causal agent of Fusarium wilt of eggplant. Genome Announc 5:e01597-16. https://doi.org/10.1128/genomeA.01597-16.
REFERENCES
- 1.Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, et al. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464:367–373. doi: 10.1038/nature08850. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Matuo T, Ishigami K. 1958. On the wilt of Solanum melongena L. and its causal fungus Fusarium oxysporum f. melongenae n. f. Jpn J Phytopathol 23:189–192. doi: 10.3186/jjphytopath.23.189. [DOI] [Google Scholar]
- 3.Zhuang WY, Guo L, Guo SY, Guo YL, Mao XL, Sun SX, Wei SX, Wen HA, Yu ZH, Zhang XQ, Zhuang JY. 2005, Fungi of northwestern China. Mycotaxon, Ithaca, NY. [Google Scholar]
- 4.Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi: 10.1101/gr.074492.107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117–1123. doi: 10.1101/gr.089532.108. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18. doi: 10.1186/2047-217X-1-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Stanke M, Steinkamp R, Waack S, Morgenstern B. 2004. AUGUSTUS: a Web server for gene finding in eukaryotes. Nucleic Acids Res 32:W309–W312. doi: 10.1093/nar/gkh379. [DOI] [PMC free article] [PubMed] [Google Scholar]