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.
Highlights
A very adaptable and economical source of protein available to mankind is legumes
The list of predicted Transcription factors (TFs) of these 30 fungal species was extracted from DNA-binding domain (DBD): a TF prediction database (Wilson et al, 2008) and Fungal Transcription Factor Database (FTFD) (Park et al, 2008)
Sixteen putative TFs that failed to show any match in FTFD database were searched in NCBI database and were selected if they displayed significant homology with any known TF
Summary
A very adaptable and economical source of protein available to mankind is legumes. Apart from having high nutritional value, legumes serve as great natural soil fertilizers. They provide nitrogen to the crops by fixing atmospheric nitrogen, thereby, decreasing the use of artificial nitrogen fertilizers. This minimizes the side effects that artificial fertilizers impose on our environment. Like all plants, legumes are challenged by various biotic and abiotic stresses causing major yield loss worldwide. The defense responses of plants in combating these environmental stresses are crucial for completing their lifecycle successfully
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