Draft genome sequencing and secretome profiling of Sclerotinia sclerotiorum revealed effector repertoire diversity and allied broad-host range necrotrophy

Abstract

White mold commonly known as Sclerotinia sclerotiorum causes stem rot disease and has emerged as one of the major fungal pathogens of oilseed Brassica across the world. In the present study, consistently virulent S. sclerotiorum isolate “ESR-01” was sequenced and an assembly size of ~ 41 Mb with 328 scaffolds having N50 of 447,128 was obtained. Additionally, 27,450 single nucleotide polymorphisms (SNPs) were identified from 155 scaffolds against S. sclerotiorum 1980 isolate, with an average SNP density of ~ 1.5 per kb genome. 667 repetitive elements were identified and approximately comprised 7% of the total annotated genes. The DDE_1 with 454 in numbers was found to be the most abundant and accounts for 68% of the total predicted repetitive elements. In total, 3844 simple sequence repeats are identified in the 328 scaffolds. A total of 9469 protein-coding genes were predicted from the whole genome assembly with an average gene length of 1587 bp and their distribution as 230.95 genes per Mb in the genome. Out of 9469 predicted protein-coding genes, 529 genes were observed encoding the CAZymes (Carbohydrate-Active enzymes) capable of degradation of the complex polysaccharides. Glycosyltransferase (GT) families were most abundant (49.71%) among the predicted CAZymes and GT2 (23%), GT4 (20%), and glycoside hydrolase (GH) 23% with GH18 (11%) were the prominent cell wall degrading enzyme families in the ESR-01 secretome. Besides this, 156 genes essential for the pathogen-host interactions were also identified. The effector analysis in the whole genome proteomics dataset revealed a total of 57 effector candidates (ECs) and 27 of them were having their analogs whereas the remaining 30 were novel ones. Eleven selected ECs were validated experimentally by analyzing the expression profile of the ESR-01 isolate of S. sclerotiorum. Together, the present investigation offers a better understanding of the S. sclerotiorum genome, secretome, and its effector repertoire which will help in refining the present knowledge on S. sclerotiorum-Brassica interactions and necrotrophic lifestyle of the phytopathogen in general.

Population and genome-wide association studies of Sclerotinia sclerotiorum isolates collected from diverse host plants throughout the United States

“…A relatively small number of effector proteins have been characterized up to this point [reviewed in Derbyshire et al (2022) and Xu et al (2018) ]. In general, most of these studies have identified putative effectors using assays for necrosis-inducing activity on host plants, mutagenesis of S. sclerotiorum , or bioinformatic prediction of candidate effectors, often combined with identification of genes differentially regulated during infection ( Bashi et al, 2010 ; Guyon et al, 2014 ; Lyu et al, 2016 ; Yu et al, 2016 ; Westrick et al, 2019 ; Tang et al, 2020 ; Fan et al, 2021 ; Gupta et al, 2022 ; Wei et al, 2022 ; Newman et al, 2023 ). No procedures for making crosses between isolates have been developed, precluding the use of bi-parental mapping approaches to identify genetic loci influencing aggressiveness.…”

Utilization of crop wild relatives for biotic and abiotic stress management in Indian mustard [Brassica juncea (L.) Czern. & Coss.]

“…S. sclerotiorum is a broad host range phytopathogen which overpowers the plant defense mechanism through their interacting virulence factors (Rodriguez-Moreno et al, 2018). Recently, Gupta et al (2022) reported the draft genome sequence of S. sclerotiorum "ESR-01", an Indian isolate, and its secretory effector repertoire. It highlights the secretome, effector, carbohydrate active enzymes and PHI-base repertoire associated with the S. sclerotiorum genome.…”

Fungal effectors versus defense-related genes of B. juncea and the status of resistant transgenics against fungal pathogens

“…The ssv263 is an identified orthologue of B. cinerea protein and putatively reported to inflict symptoms in B. napus , though the mechanism remains unclear ( Liang et al., 2013 ). Gupta et al. (2022) did a whole genome-sequencing of a highly virulent isolate of S. sclerotiorum , “ESR-01” which yielded 57 candidate effectors, out of which 30 were reported to be novel.…”