Comparative transcriptome analyses and genome assembly of Fusarium oxysporum f. sp. cubense

M.A. Dita, R. Herai, C. Waalwijk, M. Yamagishi, P. Giachetto, G. Ferreira, M. de Souza, G.H.J. Kema

Research output: Chapter in Book/Report/Conference proceedingConference paper

Abstract

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
Original languageEnglish
Title of host publicationInternational ISHS-ProMusa Symposium on Bananas and Plantains: Towards Sustainable Global Production and Improved Use
EditorsI. van den Bergh, E.P. Amorim, V. Johnson
Place of PublicationLeuven
PublisherISHS
Pages165-168
Volume986
ISBN (Print)9789066053595
DOIs
Publication statusPublished - 2013
EventInternational ISHS-ProMusa Symposium on Bananas and Plantains: Towards Sustainable Global Production and Improved Use, Salvador (Bahia), Brazil -
Duration: 10 Oct 201114 Oct 2011

Conference

ConferenceInternational ISHS-ProMusa Symposium on Bananas and Plantains: Towards Sustainable Global Production and Improved Use, Salvador (Bahia), Brazil
Period10/10/1114/10/11

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    Dita, M. A., Herai, R., Waalwijk, C., Yamagishi, M., Giachetto, P., Ferreira, G., de Souza, M., & Kema, G. H. J. (2013). Comparative transcriptome analyses and genome assembly of Fusarium oxysporum f. sp. cubense. In I. van den Bergh, E. P. Amorim, & V. Johnson (Eds.), International ISHS-ProMusa Symposium on Bananas and Plantains: Towards Sustainable Global Production and Improved Use (Vol. 986, pp. 165-168). ISHS. https://doi.org/10.17660/ActaHortic.2013.986.17