Pathogen Virulence in Sugarcane Red Rot Pathogen Versus Varieties in Cultivation: Classical Case of Loss in Virulence in the Pathotype CF06 (Cf671)

Phylogenetic Analysis and Genetic Diversity of Colletotrichum falcatum Isolates Causing Sugarcane Red Rot Disease in Bangladesh

Simple Summary

Sugarcane is an important agro-industrial crop because it is one of the major sources of white sugar. Red rot which is caused by Colletotrichum falcatum is the most devastating disease of sugarcane because its infestation results in significant sugarcane yield loss. The intra- and inter-specific genetic diversity, population structure and phylogenetic relationship amongst C. falcatum isolates from Bangladesh remain unclear. This information is essential for the effective management of red rot and to also develop resistant sugarcane varieties through plant breeding programmes. This paper demonstrates the phylogenetic relationship and genetic diversity of C. falcatum isolates from Bangladesh. Also, it provides baseline information that can be used to establish red rot disease management strategies for future application.

Abstract

Colletotrichum falcatum Went causes red rot disease in sugarcane farming in the tropical and sub-tropical regions. This disease causes significant economic loss to the sugarcane production industry. Successful disease management strategies depend on understanding the evolutionary relationship between pathogens, genetic diversity, and population structure, particularly at the intra-specific level. Forty-one isolates of C. falcatum were collected from different sugarcane farms across Bangladesh for molecular identification, phylogeny and genetic diversity study. The four genes namely, ITS-rDNA, β-tubulin, Actin and GAPDH sequences were conducted. All the 41 C. falcatum isolates showed a 99–100% similarity index to the conserved gene sequences in the GenBank database. The phylogram of the four genes revealed that C. falcatum isolates of Bangladesh clustered in the same clade and no distinct geographical structuring were evident within the clade. The four gene sequences revealed that C. falcatum isolates from Bangladesh differed from other countries´ isolates because of nucleotides substitution at different loci. The genetic structure of C. falcatum isolates were determined using ISSR marker generated 404 polymorphic loci from 10 selected markers. The percentage of polymorphic loci was 99.01. The genetic variability at species level was slightly higher than at population level. Total mean gene diversity at the species level was 0.1732 whereas at population level it was 0.1521. The cluster analysis divided 41 isolates into four main genetic groups and the principal component analysis was consistent with cluster analysis. To the best of our knowledge, this is the first finding on characterizing C. falcatum isolates infesting sugarcane in Bangladesh. The results of this present study provide important baseline information vis a vis C. falcatum phylogeny analysis and genetic diversity study.

A highly contiguous reference genome assembly for Colletotrichum falcatum pathotype Cf08 causing red rot disease in sugarcane

Among the biotic factors, which affect the productivity and quality of sugarcane, red rot disease caused by the fungal pathogen, Colletotrichum falcatum is the most devastating that cause enormous loss to millers as well as cane growers. We present a highly contiguous genome assembly of C. falcatum pathotype Cf08 which is virulent to popular sugarcane varieties grown in more than 3 million hectares in sub-tropical India. By performing long read sequencing on PacBio RSII system, 56.06 Mb assemblies with 238 contigs having N50 of 0.51 Mb and L50 of 34 was produced. A BUSCO completeness score of 97.24% (including 4.1% fragmented) of the entire C. falcatum Cf08 nuclear genome, greatly improved contiguity compared to an existing highly fragmented draft of C. falcatum Cf671 genome (48.13 Mb) was obtained. This Cf08 assembly had 54.14% GC content and possessed < 1% repetitive elements. A total of 18,635 protein-coding genes were predicted compared with 12,270 for Cf671. Among 617 CAZymes predicted, glycoside hydrolases were the predominant (298), and among 7264 genes associated with pathogenicity/virulence, 77 genes having effector functions were identified. The assembled genome showed its similarity with the genome of C. graminicola and C. higginsianum, the causal organisms of anthracnose in maize and in members of Brassicaceae, respectively. A total of 94 large sequences (> 100 kb) of Cf08 were mapped over C. higginsianum 10 of 12 chromosomes with 106 synteny blocks. Results discussed here would provide an important tool for future studies of evolutionary and functional genomics in C. falcatum.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02695-x.

Development and characterization of genomic SSR marker for virulent strain-specific Colletotrichum falcatum infecting sugarcane

Colle totrichum falcatum, an intriguing pathogen causing red rot in sugarcane, exhibits enormous variation for pathogenicity under field conditions. A species-specific marker is very much needed to classify the virulence among the varying population and to identify the potential of a pathotype by mining the microsatellites, which are considered to be the largest genetic source to develop molecular markers for an organism. In this study, we have mined the C. falcatum genome using MISA database which yielded 12,121 SSRs from 48.1 Mb and 2745 SSRs containing sequences. The most frequent SSR types from the genome of C. falcatum was di-nucleotide which constitutes 50.89% followed by tri-nucleotide 39.60%, hepta-nucleotide 6.7%, hexa-nucleotide 1.38% and penta-nucleotide 1.3%. Over 90 SSR containing sequences from the genome were predicted using BlastX which are found to be non-homologs. Most of the annotated SSR containing sequences fell in CAZy superfamilies, proteases, peptidases, plant cell wall degrading enzymes (PCDWE) and membrane transporters which are considered to be pathogenicity gene clusters. Among them, glycosyl hydrolases (GH) were found to be abundant in SSR containing sequences which again proved our previous transcriptome results. Our in-silico results suggested that the mined microsatellites from C. falcatum genome show absence of homolog sequences which suggests that these markers could be used as an ideal species-specific molecular marker. Two virulence specific markers were characterized using conventional PCR assays from C. falcatum along with virulent species-specific (VSS) marker developed for C. gloeosporioides. The study lays the foundation for the development of C. falcatum specific molecular marker to phenotype the pathotypes based on virulence.

Field evaluation ratified by transcript and computational analyses unveils myco-protective role of SUGARWIN proteins in sugarcane

Nine elite sugarcane genotypes (SPF-234, CPF-246, CPF-247, CPF-248, HSF-240, CP-77-400, S-2006-US-658, S-2003-US-127 and S-2006-US-633) were assessed for field level tolerance against Colletotrichum falcatum followed by quantitative expression and computational analyses of mycoprotective proteins. Plug inoculation method was used to assess level of tolerance of aforementioned genotypes while growing in the field. Genotype S-2006-US-658 was categorized as resistant whereas genotypes CPF-246, CPF-248, HSF-240, S-2003-US-127, S-2006-US-633 and CP-77-400 were categorized as moderately resistant and genotypes SPF-234, CPF-247 as moderately susceptible. Quantitative transcript analyses also revealed that the expression of mycoprotective genes (SUGARWIN1 and SUGARWIN2) was maximum in genotype CPF-246 whereas lowest in genotype SPF-234. Hence these mycoprotective proteins play some critical role in fungal pathogen protection as genotypes with higher expression are more tolerant compared to the genotypes with lower expression of mycoprotective proteins. In-silico interaction of these mycoprotective proteins with chitin, glucan, chitosan and mannan (the core constituents of fungal cell wall) also validated their role in disease susceptibility or resistance. These studies will prove a step forward in understanding mycoprotective proteins and can be employed to develop molecular markers for the selection and screening of red rot resistant sugarcane varieties resulting in enhanced productivity of this valuable cash crop.

Molecular identification and biocontrol activity of sugarcane rhizosphere bacteria against red rot pathogen Colletotrichum falcatum

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A total of 226 isolates were screened against three strains (cfNAV, cfCHA and cf8436) of C. falcatum by dual culture technique. Selected Twenty-Six bacteria characterized of morphology, biochemical activity, PGP activity, antifungal potential and 16S rRNA gene sequence. These isolates belonged to proteobacteria (13), firmicutes (10) and bacterioidetes (03) respectively.

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Ochrobactrum intermedium (TRD14), Acinetobacter sp (PK9), Bacillus sp (RSC29 and KR91) and Escherichia sp (VRE34) selected for green house study. The most promising results in suppression of the disease as well as plant growth were observed in treatment withVRE34. The plant height and stem diameter were increased from 13.27 ± 0.67 inches to 24.03 ± 1.40 inches and from 6.07 ± 0.45 mm to 9.87 ± 0.93 mm.

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Isolates identified in this study could be used as an alternative to chemical fungicides to control red rot pathogen of sugarcane plants. However, detailed investigations on their inoculations in the field to confirm its growth promotion potency and biocontrol efficacy under natural environmental and soil conditions shall make these strains as important bioinoculants for integrated disease management of red rot disease in sugarcane.

A total of 226 sugarcane rhizosphere-associated bacterial strains from the six different cultivars were screened against three pathogenic strains of C. falcatum (cfNAV, cfCHA, and cf8436) for the suppression of red rot disease. On the basis of mycelial growth inhibition in dual culture assay, 26 bacteria were selected for further characterization of morphology, biochemical activity, plant-growth-promoting (PGP) activity, antifungal potential and molecular identity by 16S rRNA gene sequence. On the basis of the 16S rRNA gene sequencing, it was found that the isolates belonged to proteobacteria (13), Firmicutes (10), and Bacteroides (3). The antagonistic bacteria tested for PGP traits revealed that 10 strains were able to solubilize tricalcium phosphate, 11 strains were able to produce siderophore, and 14 strains were able to grow in the N-free medium. The quantitative estimation of indole-3-acetic acid production was ranged from 21.58 to 66.31 μg/mL. On the basis of PGP and biocontrol traits, five strains Ochrobactrum intermedium (TRD14), Acinetobacter sp. (PK9), Bacillus sp. (RSC29 and KR91) and Escherichia sp. (VRE34) were further chosen for pot trial under greenhouse conditions on highly susceptible variety CoC671. The results showed that the pathogen-inoculated sugarcane plants were able to germinate but died within one month. However, the CoC671 inoculated with selected biocontrol strains found protected from disease and an increase in plant growth parameters on par with carbendazim fungicides. This study proves that the isolates identified in this study could be used as an alternative to chemical fungicides to control red rot pathogen of sugarcane plants.

CfPDIP1, a novel secreted protein of Colletotrichum falcatum, elicits defense responses in sugarcane and triggers hypersensitive response in tobacco

Colletotrichum falcatum, a hemibiotrophic fungal pathogen, causes one of the major devastating diseases of sugarcane-red rot. C. falcatum secretes a plethora of molecular signatures that might play a crucial role during its interaction with sugarcane. Here, we report the purification and characterization of a novel secreted protein of C. falcatum that elicits defense responses in sugarcane and triggers hypersensitive response (HR) in tobacco. The novel protein purified from the culture filtrate of C. falcatum was identified by MALDI TOF/TOF MS and designated as C. falcatum plant defense-inducing protein 1 (CfPDIP1). Temporal transcriptional profiling showed that the level of CfPDIP1 expression was greater in incompatible interaction than the compatible interaction until 120 h post-inoculation (hpi). EffectorP, an in silico tool, has predicted CfPDIP1 as a potential effector. Functional characterization of full length and two other domain deletional variants (CfPDIP1ΔN1-21 and CfPDIP1ΔN1-45) of recombinant CfPDIP1 proteins has indicated that CfPDIP1ΔN1-21 variant elicited rapid alkalinization and induced a relatively higher production of hydrogen peroxide (H2O2) in sugarcane suspension culture. However, in Nicotiana tabacum, all the three forms of recombinant CfPDIP1 proteins triggered HR along with the induction of H2O2 production and callose deposition. Further characterization using detached leaf bioassay in sugarcane revealed that foliar priming with CfPDIP1∆1-21 has suppressed the extent of lesion development, even though the co-infiltration of CfPDIP1∆1-21 with C. falcatum on unprimed leaves increased the extent of lesion development than control. Besides, the foliar priming has induced systemic expression of major defense-related genes with the concomitant reduction of pathogen biomass and thereby suppression of red rot severity in sugarcane. Comprehensively, the results have suggested that the novel protein, CfPDIP1, has the potential to trigger a multitude of defense responses in sugarcane and tobacco upon priming and might play a potential role during plant-pathogen interactions.

Antifungal activity of chitinase II against Colletotrichum falcatum Went. causing red rot disease in transgenic sugarcane

We evaluated transgenic lines of sugarcane modified with the barley chitinase class-II gene to create resistance against the red rot causative agent Colletotrichum falcatum Went. Local sugarcane cultivar SP93 was transformed with a 690-bp coding sequence of the chitinase-II gene under the influence of a polyubiquitin promoter. Transgenic sugarcane lines (T 0) overexpressing the chitinase gene were obtained through a particle bombardment method with 13.3% transformation efficiency. Four transgenic sugarcane lines, SCT-03, SCT-05, SCT-15, and SCT-20, were tested for resistance against red rot by in vitro antifungal assays. Crude protein extracts from transgenic sugarcane plants SCT-03, SCT-05, SCT-15, and SCT-20 inhibited the mycelial growth of C. falcatum by 49%, 40%, 56%, and 52%, respectively, in a quantitative in vitro assay. Our findings revealed that two transgenic lines, SCT-15 and SCT-20, exhibited the highest endochitinase activity of 0.72 and 0.58 U/mL, respectively. Furthermore, transgenic lines SCT-15 and SCT-20 exhibited strong resistance against inoculated C. falcatum in an in vitro bioassay, as they remained healthy and green in comparison with the control sugarcane plants, which turned yellow and eventually died 3 weeks after infection. The mRNA expression of the transgene in the C. falcatum-inoculated transgenic sugarcane lines increased gradually compared to the control plant. The mRNA expression was the highest at 72 h in both transgenic lines and remained almost stable in the subsequent hours.