Senior Research Fellow, ICAR-SUGARCANE BREEDING INSTITUTE
Colletotrichum, a complex species with broad host range and economically important plant pathogen.
Colletotrichum, a highly studied group of fungi which is considered to be the model organism for plant pathogen interaction and also it causes economic impact by their members of the family. The interaction between the plant and the pathogen is highly influenced by the CSEPs which are the key precursor in stage shift of Colletotrichum spp. Colletotrichum falcatum Went (Perfect state; Glomerella tucumanensis (Speg.) Arx & Muller) infects the cane stalks and causes symptoms of tissue discoloration, inversion of sucrose due to production of pathogen induced invertases and drying of cane stalks. It is one of the most widespread sugarcane diseases during the early years of the last century in many countries is attested by the numerous references to its economic importance. However, the molecular tools have yet to be fully explored to characterize the genes activated during pathogen invasion. Recently the whole genome of C. falcatum was sequenced through Illumina Hi Seq 2500 platform, the raw reads were assembled into contigs and scaffolds using Velvette and SSpace. The assembled scaffolds and contigs yielded 48.16 Mb genome with 12270 genes majorly having syntenic relationship with C. graminicola, C. sublineola, C. higginsianum, C. gloeosporioides, C. fructicola, and C. orbiculare. To understand much about the genes which attribute to pathogenicity and to analyse the lifestyle transition of C. falcatum, an application of high throughput sequencing based transcriptome analyses of sugarcane challenged with C. falcatum revealed that even though genomic structure of other Colletotrichum species was quite similar. The distinctive gene families with specific gene loss and expansion attributes to pathogenicity determines the specific infection lifestyle among species of Colletotrichum. The major class of genes plays a pivotal role in virulence and lifestyle transition of Colletotrichum can be grouped into four classes namely CSEPs, Secondary Metabolites, CAZy and Membrane Transporters. The C. falcatum genome and transcriptome have revealed several putative genes which is involved in fungal pathogenicity determinants and stage specific genes (Biotrophic phase genes – Necrotrophic phase genes). These finding provides a better understanding in the roles of these genes involved in virulence and a beginning in elucidating the mechanism of fungal biology and deciphering the lifestyle of the pathogen.
Abstract: Red rot, a stalk disease in sugarcane caused by Colletotrichum falcatum an ascomycete fungus is a serious production constraint in many Asian countries. However, very limited studies at molecular level exist of the mechanisms related to interaction between sugarcane and the fungal pathogen C. falcatum (Cf). In the conventional system of pathogen inoculation, disease development is influenced by prevailing environmental conditions in the field. Hence an attempt was made to standardize an in vitro system of using sugarcane suspension cells and crude elicitor of Cf for transcriptome analysis and identifying defense related genes. Suspension cells of sugarcane cv Co 93009 was treated with Cf-elicitor at 60 glucose equivalents and transcriptome profile was monitored 30 min and 3 h later by differential display RT-PCR. From the experiment 241 transcripts were found to be differentially expressed and finally 75 of them were cloned and sequenced. Among the up-regulated transcripts, about 37 % were found to be defense related and which was followed by transcription and post transcription (13 %), general metabolism (11 %), transport (9 %), cell structure/growth/division (9 %) and signal transduction (5 %). The down regulated transcript group constituted ~27 % of the differentially expressed transcripts and the grouping pattern was different. Overall, the results revealed up regulation of many potential defense related transcripts like putative chitinase, glycine rich protein, 14-3-3-like protein, xylanase inhibitor protein, calmodulin related protein, Myb-related transcription factor CBM2-like, basal layer antifungal peptide etc. Further by adopting RACE-PCR approach, complete gene sequences of 14-3-3-like protein and xylanase inhibitor were identified and the genes were characterized to domain level. Our results demonstrate that the transcript profile in in vitro system of sugarcane suspension cells and Cf-elicitor is close to the cane tissue challenged with the pathogen and useful to identify defense related traits in sugarcane against Cf.
Pub.: 22 Nov '14, Pinned: 26 Aug '17
Abstract: Colletotrichum falcatum, a concealed fungal ascomycete causes red rot, which is a serious disease in sugarcane. It infects economically important stalk tissues, considered as store house of sugar in sugarcane. The study is to find genetic complexities of C. falcatum in establishing this as a stalk infecting pathogen and to decipher the unique lifestyle of this pathogen using NGS technology. We report the draft genome of C. falcatum of about 48.16 Mb in size with 12,270 genes. The genome sequences were compared with other fungal species which revealed that C. falcatum is closely related to C. graminicola and C.sublineola the causal organisms of anthracnose in maize and sorghum. These results brought a new revelation to explore the lifestyle of this unique pathogen which is specialized to infect sugarcane stalk tissues in detail.
Pub.: 10 Mar '16, Pinned: 26 Aug '17