title: Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.
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.
authors.affiliation: The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia. Angela.Williams2@csiro.au.|CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Angela.Williams2@csiro.au.
authors.forename: Angela H
authors.initials: AH
authors.lastname: Williams
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India. mamta.sharma@CGIAR.ORG.
authors.forename: Mamta
authors.initials: M
authors.lastname: Sharma
authors.affiliation: CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Louise.Thatcher@csiro.au.
authors.forename: Louise F
authors.initials: LF
authors.lastname: Thatcher
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India. shrisarwarazam@gmail.com.
authors.forename: Sarwar
authors.initials: S
authors.lastname: Azam
authors.affiliation: CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. james.hane@curtin.edu.au.|Department of Environment and Agriculture, Curtin Institute for Computation, and CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Perth, WA, 6102, Australia. james.hane@curtin.edu.au.
authors.forename: James K
authors.initials: JK
authors.lastname: Hane
authors.affiliation: CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Jana.Sperschneider@csiro.au.
authors.forename: Jana
authors.initials: J
authors.lastname: Sperschneider
authors.affiliation: CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Brendan.Kidd@csiro.au.
authors.forename: Brendan N
authors.initials: BN
authors.lastname: Kidd
authors.affiliation: The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia. Jonathan.Anderson@csiro.au.|CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Jonathan.Anderson@csiro.au.
authors.forename: Jonathan P
authors.initials: JP
authors.lastname: Anderson
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India. r.ghosh@cgiar.org.
authors.forename: Raju
authors.initials: R
authors.lastname: Ghosh
authors.affiliation: CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Gagan.Garg@csiro.au.
authors.forename: Gagan
authors.initials: G
authors.lastname: Garg
authors.affiliation: Department of Environment and Agriculture, Pulse Pathology and Genetics, Centre for Crop and Disease Management and Curtin Institute for Computation, Curtin University, Perth, WA, 6102, Australia. Judith.Lichtenzveig@curtin.edu.au.
authors.forename: Judith
authors.initials: J
authors.lastname: Lichtenzveig
authors.affiliation: USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA. hckist@umn.edu.
authors.forename: H Corby
authors.initials: HC
authors.lastname: Kistler
authors.affiliation: The Broad Institute, Cambridge, MA, 02141, USA. tshea@broadinstitute.org.
authors.forename: Terrance
authors.initials: T
authors.lastname: Shea
authors.affiliation: The Broad Institute, Cambridge, MA, 02141, USA. sarah@broadinstitute.org.
authors.forename: Sarah
authors.initials: S
authors.lastname: Young
authors.affiliation: CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. 21130902@student.uwa.edu.au.
authors.forename: Sally-Anne G
authors.initials: SA
authors.lastname: Buck
authors.affiliation: The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia. Lars.Kamphuis@csiro.au.|CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Lars.Kamphuis@csiro.au.
authors.forename: Lars G
authors.initials: LG
authors.lastname: Kamphuis
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India. R.Saxena@cgiar.org.
authors.forename: Rachit
authors.initials: R
authors.lastname: Saxena
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India. s.pande@cgiar.org.
authors.forename: Suresh
authors.initials: S
authors.lastname: Pande
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA. lijun@biochem.umass.edu.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Ma
authors.affiliation: The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia. R.K.Varshney@CGIAR.ORG.|International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India. R.K.Varshney@CGIAR.ORG.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia. Karam.Singh@csiro.au.|CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia. Karam.Singh@csiro.au.
authors.forename: Karam B
authors.initials: KB
authors.lastname: Singh
mesh_terms: D055028:Comparative Genomic Hybridization; D017124:Conserved Sequence; D004271:DNA, Fungal / Q000235:genetics; D007887:Fabaceae / Q000382:microbiology*; D005656:Fungal Proteins / Q000235:genetics; D005670:Fusarium / Q000145:classification / Q000235:genetics*; D016681:Genome, Fungal; D058507:Host Specificity; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins