Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome

Abstract

Transcription factors (TFs) are the key players in gene expression and their study is highly significant for shedding light on the molecular mechanisms and evolutionary history of organisms. During host–pathogen interaction, extensive reprogramming of gene expression facilitated by TFs is likely to occur in both host and pathogen. To date, the knowledge about TF repertoire in filamentous fungi is in infancy. The necrotrophic fungus Ascochyta rabiei, that causes destructive Ascochyta blight (AB) disease of chickpea (Cicer arietinum), demands more comprehensive study for better understanding of Ascochyta-legume pathosystem. In the present study, we performed the genome-wide identification and analysis of TFs in A. rabiei. Taking advantage of A. rabiei genome sequence, we used a bioinformatic approach to predict the TF repertoire of A. rabiei. For identification and classification of A. rabiei TFs, we designed a comprehensive pipeline using a combination of BLAST and InterProScan software. A total of 381 A. rabiei TFs were predicted and divided into 32 fungal specific families of TFs. The gene structure, domain organization and phylogenetic analysis of abundant families of A. rabiei TFs were also carried out. Comparative study of A. rabiei TFs with that of other necrotrophic, biotrophic, hemibiotrophic, symbiotic, and saprotrophic fungi was performed. It suggested presence of both conserved as well as unique features among them. Moreover, cis-acting elements on promoter sequences of earlier predicted A. rabiei secretome were also identified. With the help of published A. rabiei transcriptome data, the differential expression of TF and secretory protein coding genes was analyzed. Furthermore, comprehensive expression analysis of few selected A. rabiei TFs using quantitative real-time polymerase chain reaction revealed variety of expression patterns during host colonization. These genes were expressed in at least one of the time points tested post infection. Overall, this study illustrates the first genome-wide identification and analysis of TF repertoire of A. rabiei. This work would provide the basis for further studies to dissect role of TFs in the molecular mechanisms during A. rabiei–chickpea interactions.

Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome

“…In this study, the MYB gene family of P. ostreatus was analyzed at the genome-wide level . P. ostreatus has 20 MYB genes, which is more than that of Magnaporthe oryzae (13), Botrytis cinerea (15), Ascochyta rabiei (16), and Fusarium graminearum (19) [ 56 ], and less than that of Neurospora crassa (36) and Laccaria bicolor (37) [ 57 ]. The size of the MYB gene family of P. ostreatus is smaller than those of plants, but larger than those of animals, which generally comprise four or five MYBs [ 58 ].…”

Reference Genome Assembly for AustralianAscochyta rabieiIsolate ArME14

“…There were 323 putative effectors with no known protein domain and 70 proteins of the predicted secretome showed sequence similarity to members of the Pathogen-Host Interaction (PHI) database (Winnenburg et al 2006) with annotated involvement in virulence or pathogenicity (Verma et al 2016). In addition to proposed virulence proteins, transcription factors that control gene expression during plant infection by A. rabiei have been predicted for ArD2 and assessed for their contribution to pathogenesis (Verma et al 2017). Verma et al (2017) suggest that for A. rabiei, Myb transcription factors play a role in regulating the expression of genes encoding secreted proteins, such as effectors.…”

“…In addition to proposed virulence proteins, transcription factors that control gene expression during plant infection by A. rabiei have been predicted for ArD2 and assessed for their contribution to pathogenesis (Verma et al 2017). Verma et al (2017) suggest that for A. rabiei, Myb transcription factors play a role in regulating the expression of genes encoding secreted proteins, such as effectors. Gene regulation by transcription factors during plant infection may also vary depending on specific isolate and host interactions (Verma et al 2017).…”

“…Verma et al (2017) suggest that for A. rabiei, Myb transcription factors play a role in regulating the expression of genes encoding secreted proteins, such as effectors. Gene regulation by transcription factors during plant infection may also vary depending on specific isolate and host interactions (Verma et al 2017).…”

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

“…For example, genes M_11_12_v1_01448 and M11_12_v1_01460 are both likely transcription factors with Pfam domains including the Myb-like DNA binding domain and the Zn(2)-Cys(6) binuclear cluster domain, respectively. Previous research has shown that transcription factors with the Myb-like DNA binding domain regulate the secretome in necrotrophic fungal pathogen [31] and a transcription factor with the Zn(2)-Cys(6) binuclear cluster domain has a key role in regulating virulence in a fungus infecting wheat [32]. The cytochrome P450 gene, M11_12_v1_01466, is a member of a large group of genes that was found to be present in the M. phaseolina genome in high numbers and may be associated with secondary metabolites and overcoming hose defenses [1].…”