Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

Williams, A H and Sharma, M and Thatcher, L F and Azam, S and Hane, J K and Sperschneider, J and Kidd, B N and Anderson, J P and Ghosh, R and Garg, G and Lichtenzveig, J and Kistler, H C and Shea, T and Young, S and Buck, S G and Kamphuis, L G and Saxena, R K and Pande, S and Ma, L J and Varshney, R K and Singh, K B (2016) Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics, 17 (191). 01-24. ISSN 1471-2164

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Abstract

Abstract Background Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world’s second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. Results Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. Conclusions We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn’t share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Fusarium, Conditionally dispensable chromosomes (CDC), Effectors, Pathogenicity, Legume, Pulse, Fungal pathogen, Genomics, Legumes
Subjects: Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 14 Mar 2016 09:15
Last Modified: 21 Oct 2016 05:45
URI: http://oar.icrisat.org/id/eprint/9383
Official URL: http://dx.doi.org/10.1186/s12864-016-2486-8
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: Data sources and acknowledgements This research was undertaken with the assistance of resources from the Australian Genome Research Facility (AGRF) and the National Computational Infrastructure Specialised Facility for Bioinformatics (NCI-SF Bioinformatics), which are both supported by the Australian Government. The work was supported by iVEC through the use of advanced computing resources located at the Pawsey Supercomputing Centre. Data used for comparative analysis was obtained from NCBI, unpublished Fusarium data sets obtained from “Fusarium Comparative Sequencing Project, Broad Institute of Harvard and MIT (http://​www.​broadinstitute.​org/​)”, Broad Institute Genomics Platform, Feb 2014. F. solani and F. fujikuoroi data was obtained from the JGI Genome portal (http://​genome.​jgi.​doe.​gov/​), all data sources are outlined in Additional file 4 . We also thank Elaine Smith for excellent technical assistance and Dr Donald Gardiner for critical reading of the manuscript and useful suggestions.
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