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Background  Pathogenic members of the  Fusarium oxysporum  species complex are responsible for vascular wilt disease on many important crops including legumes, where they can be one of the most destructive disease causing necrotrophic fungi. We previously developed a model legume-infecting pathosystem based on the reference legume  Medicago truncatula  and a pathogenic  F. oxysporum  forma specialis (f. sp.)  medicaginis  ( Fom ). To dissect the molecular pathogenicity arsenal used by this root-infecting pathogen, we sequenced its transcriptome during infection of a susceptible and resistant host accession.    Results  High coverage RNA-Seq of  Fom  infected root samples harvested from susceptible (DZA315) or resistant (A17)  M. truncatula  seedlings at early or later stages of infection (2 or 7 days post infection (dpi)) and from vegetative (in vitro) samples facilitated the identification of unique and overlapping sets of  in planta  differentially expressed genes. This included enrichment, particularly in DZA315  in planta  up-regulated datasets, for proteins associated with sugar, protein and plant cell wall metabolism, membrane transport, nutrient uptake and oxidative processes. Genes encoding effector-like proteins were identified, including homologues of the  F. oxysporum  f. sp.  lycopersici  Secreted In Xylem (SIX) proteins, and several novel candidate effectors based on predicted secretion, small protein size and high  in-planta  induced expression. The majority of the effector candidates contain no known protein domains but do share high similarity to predicted proteins predominantly from other  F. oxysporum  ff. spp. as well as other  Fusaria  ( F. solani, F. fujikori, F. verticilloides, F. graminearum  and  F. pseudograminearum ), and from another wilt pathogen of the same class, a  Verticillium  species. Overall, this suggests these novel effector candidates may play important roles in  Fusaria  and wilt pathogen virulence.    Conclusion  Combining high coverage  in planta  RNA-Seq with knowledge of fungal pathogenicity protein features facilitated the identification of differentially expressed pathogenicity associated genes and novel effector candidates expressed during infection of a resistant or susceptible  M. truncatula  host. The knowledge from this first in depth  in planta  transcriptome sequencing of any  F. oxysporum  ff. spp. pathogenic on legumes will facilitate the dissection of  Fusarium  wilt pathogenicity mechanisms on many important legume crops.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3192-2) contains supplementary material, which is available to authorized users.

bmc genomics

Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors