Comparative Transcriptome Analyses And Genome Assembly Of Fusarium Oxysporum F. Sp. Cubense

Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt of banana, is a highly destructive and genetically diverse pathogen. Despite its economic importance, genomic information about Foc is limited and no transcriptomic analyses have been reported so far. By using 454 sequencing technology, we generated >2.5 million expressed sequenced tags (ESTs) from four Foc isolates representing different vegetative compatibility groups (VCGs) and races that infect banana: race 1 (R1, VCG unknown but different from the others here described), race 2 (R2, VCG 0124), subtropical race 4 (SR4, VCG 0120) and tropical race 4 (TR4, VCG 01213). The ESTs were obtained from libraries prepared from mRNA extracted from three physiological states (mycelium, conidia and germinated conidia), which were pooled in a 2:2:1 ratio. Most genes are represented in all libraries, but in silico comparative analyses identified a set of unique ESTs for each isolate (689 for R1, 974 for R2, 296 for SR4 and 555 for TR4), which are excellent candidates for diagnostics development, future plant-pathogen interaction studies and functional analyses. In subsequent analyses, a 40× sequencing-coverage (Illumina single reads) of TR4 genomic DNA was assembled in a de novo based methodology, resulting in a 45.5 Mb genome. Preliminary analyses show a high colinearity of EST and genomic data that significantly contributes to the quality of the assembly.986167168Bentley, S., Pegg, K.G., Moore, N.Y., Davis, R.D., Buddenhagen, I.W., Genetic variation among vegetative compatibility groups of Fusarium oxysporum f. sp. cubense analyzed by DNA fingerprinting (1998) Phytopathology, 88, pp. 1283-1293Desjardins, A.E., Proctor, R.H., Bai, G.H., McCormick, S.P., Shaner, G., Buechley, G., Hohn, T.M., Reduced virulence of trichothecene-nonproducing mutants of gibberella zeae in wheat fields tests (1996) Mol. Plant Microbe in, 9, pp. 775-781Dita, M., Waalwijk, C., Buddenhagen, I.W., Souza, Jr.M.T., Kema, G.H.J., A molecular diagnostic for tropical race 4 of the banana fusarium wilt pathogen (2010) Plant Pathol, 59, pp. 348-357Fourie, G., Steenkamp, E.T., Ploetz, R.C., Gordon, T.R., Viljoen, A., Current status of the taxonomic position of fusarium oxysporum formae specialis cubense within the fusarium oxysporum complex (2011) Infect. Genet. Evol, 11, pp. 533-542Groenewald, S., Van Den Berg, N., Marasas, W.F.O., Viljoen, A., The application of high-throughput aflp's in assessing genetic diversity in fusarium oxysporum f (2006) Sp. Cubense. Mycol. Res, 110, pp. 297-305Li, H., Durbin, R., Fast and accurate short read alignment with burrows-wheeler transform (2009) Bioinformatics, 25, pp. 1754-1760Ma, L.J., Van Der Does, H.C., Borkovich, K.A., Coleman, J., Daboussi, M.J., Di Pietro, A., Comparative genomics reveals mobile pathogenicity chromosomes in fusarium (2010) Nature, 464, pp. 367-373Ploetz, R., Panama disease, an old nemesis rears its ugly head: Part 1, the beginnings of the banana export trades (2005) Plant Health Prog., , Published Online 21 December 2005doi:10.1094/PHP-2005-1221 1-RVQuinn, N.L., Levenkova, N., Chow, W., Bouffard, P., Boroevich, K.A., Knight, J.R., Assessing the feasibility of gs flx pyrosequencing for sequencing the atlantic salmon genome (2008) BMC Genomics, 9, p. 404Schulte, J.H., Marschall, T., Martin, M., Rosenstiel, P., Mestdagh, P., Schlierf, S., Deep sequencing reveals differential expression of micrornas in favorable versus unfavorable neuroblastoma (2010) Nucleic Acids Res, 38, pp. 5919-5928Wang, L., Feng, Z., Wang, X., Wang, X., Zhang, X., DEGseq: An R package for identifying differentially expressed genes from RNA-seq data (2010) Bioinformatics, 26, pp. 136-136Zerbino, D.R., Birney, E., Velvet: Algorithms for de novo short read assembly using de bruijn graphs (2008) Genet. Res, 18, pp. 821-82