Integrated RNA-seq and sRNA-seq revealed differences in transcriptome between susceptible and resistant tomato responding toFusarium oxysporum

Abstract

Tomato wilt disease caused by Fusarium oxysporum f. sp. 22 lycopersici (FOL) is a worldwide destructive disease of tomato. As exploring gene 23 expression and function approaches constitute an initial point for investigating 24 pathogen-host interaction, we performed RNA-seq and sRNA-seq analysis to 25 unravel regulated genes and miRNAs in tomato infected by FOL. Differentially 26 expressed (DE) protein coding gene and miRNA gene profiles upon inoculation 27 with FOL were presented at twenty-four hours post-inoculation including four 28 treatments. Total of more than 182.6 million and 132.2 million high quality clean 29 reads were obtained by RNA-seq and sRNA-seq, respectively. A large overlap was 30 found in DE mRNAs between susceptible cultivar Moneymaker and resistant 31 cultivar Motelle. All Gene Ontology terms were mainly classified into catalytic 32 activity, metabolic process and binding. Combining with qRT-PCR, five disease 33 resistance genes, Solyc01g095630, Solyc03g059080, Solyc00g174340, 34 Solyc11g071750 and Solyc05g050350, were verified to involved in the disease 35 resistance in the resistant cultivar Motelle treated with FOL. Northern blot analysis 36 further confirmed the results from sRNA-Seq and demonstrated that several 37 miRNAs including Sly-miR477-5p, sly-miR167a, novel_mir_675, novel_mir_504 38 and novel_mir_762 conferred FOL infection. Our data resulted that pathogen 39 resistant genes/miRNAs may play a critical role with the benefit of a coordinated 40 machinery in prompting the response in prompting FOL response in tomato, which 41 offered us with a future direction and surely help in generating models of mediated 42 resistance responses with assessment of genomic gene expression patterns. 43 KEYWARDS Tomato, Fusarium oxysporum f. sp. Lycopersici, Transcriptome, 44 Wilt disease, Resistance 45 46 100 2014). However, there was still no other reported miRNAs conferring tomato wilt 101 disease so far. In addition, there is far less attention to understand how genes and 102 miRNAs are integrated into the dynamic and complex regulatory network which 103 act together to regulate and result in the enhancement of resistance to FOL in 104 tomato. 105 The objective of this study was to determine differences between the transcript 106 profiles of susceptible Moneymaker and resistant Motelle tomato cultivars in 107 response to FOL infection and to reveal genes and miRNAs underlying the innate 108 immune response against the fungal pathogen combining RNA-seq and sRNA-seq 109 approach. In addition to genes predicted to response to pathogen infection, our 110 results also uncovered a bunch of novel fungal pathogen-responsive miRNAs in 111 tomato host plant for further functional characterization, and provided a broader 112 view of the dynamics of tomato defense triggered by FOL infection. 113 MATERIALS AND METHODS 114 Tomato materials and fungal culture 115 For tomato materials and fungal culture, susceptible cultivar Moneymaker (i-2/i-2) 116 and resistant cultivar Motelle (I-2/I-2) were applied for pl...

Transcriptional responses to Fusarium oxysporum f. sp. lycopersici (Sacc.) Snyder & Hansen infection in three Colombian tomato cultivars

“…This is consistent with a recent study, using microarrays, wherein 16 different WRKY transcription factors were found upregulated in tomato plants infected with Fol, among which WRKY36 and WRKY37 stood out [29]. Thus, it is possible that the plethora of WRKY transcription factors represents the evolution of specialized responses against different Fol strains [34,35], and more generally, against different pathogens [30]. WRKY transcription factors were not found upregulated in the cultivars CT2 or IAC391.…”