De Novo Transcriptome Sequencing and Analysis for Venturia inaequalis, the Devastating Apple Scab Pathogen

Abstract

Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.

Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

“…The number of predicted genes in the Venturia genomes (11,960–13,333) is significantly less than the 24,571 unique fungal genes reported for V. inaequalis by Thakur et al [21]. Just over half of the reported sequences had no significant similarity to sequences in other species.…”

Transcriptome analysis of a powdery mildew pathogen (Podosphaera pannosa) infecting Eucalyptus urophylla: De novo assembly, expression profiling and secretome prediction

“…This method has yielded good results for several non-model organisms, including fungi (Liu et al, 2015;Ross-Davis et al, 2013;Thakur et al, 2013;Yazawa, Kawahigashi, Matsumoto, & Mizuno, 2013) and…”

Dual RNA‐seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants

“…In the absence of a reference genome, dual RNA-seq represents a good opportunity to obtain a large amount of data on the nematode genes expressed during the biotrophic interaction with rice. The simultaneous sequencing of plant and pathogen mRNAs has been successfully applied to decipher molecular plant-pathogen interactions (Kawahara et al, 2012;Teixeira et al, 2014;Yang et al, 2013) even without the reference genome (Fernandez et al, 2012;Thakur et al, 2013;Tremblay et al, 2013). In this study, 12 transcriptomic datasets were generated from two biological replicates of six different M. graminicola life stages in rice plants from pre-parasitic J2 to adult female stages.…”