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Pathogens 9 (1): 27 (2019)
Michael Smith Laboratories
Xia, Shitou
Xu, Yan
Hoy, Ryan
Zhang, Julia
Qin, Lei
Li, Xin
Ascomycete Sclerotinia sclerotiorum (Lib.) de Bary is one of the most damaging soilborne fungal pathogens affecting hundreds of plant hosts, including many economically important crops. Its genomic sequence has been available for less than a decade, and it was recently updated with higher completion and better gene annotation. Here, we review key molecular findings on the unique biology and pathogenesis process of S. sclerotiorum, focusing on genes that have been studied in depth using mutant analysis. Analyses of these genes have revealed critical players in the basic biological processes of this unique pathogen, including mycelial growth, appressorium establishment, sclerotial formation, apothecial and ascospore development, and virulence. Additionally, the synthesis has uncovered gaps in the current knowledge regarding this fungus. We hope that this review will serve to build a better current understanding of the biology of this under-studied notorious soilborne pathogenic fungus.
pathogensReviewThe Notorious Soilborne Pathogenic FungusSclerotinia sclerotiorum: An Update on Genes Studiedwith Mutant AnalysisShitou Xia 1,*,† , Yan Xu 2,3,†, Ryan Hoy 2, Julia Zhang 4, Lei Qin 1 and Xin Li 2,3,*1 Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan AgriculturalUniversity, Changsha 410128, China; leiqin@stu.hunau.edu.cn2 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;yan.xu@msl.ubc.ca (Y.X.); rhoy@alumni.ubc.ca (R.H.)3 Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada4 School of Kinesiology, University of British Columbia, Vancouver, BC V6T 1Z1, Canada;Julia.Zhang@hli.ubc.ca* Correspondence: xstone0505@hunau.edu.cn (S.X.); xinli@msl.ubc.ca (X.L.)† These authors contributed equally to the review.Received: 29 November 2019; Accepted: 22 December 2019; Published: 27 December 2019 Abstract: Ascomycete Sclerotinia sclerotiorum (Lib.) de Bary is one of the most damaging soilbornefungal pathogens affecting hundreds of plant hosts, including many economically important crops.Its genomic sequence has been available for less than a decade, and it was recently updated withhigher completion and better gene annotation. Here, we review key molecular findings on the uniquebiology and pathogenesis process of S. sclerotiorum, focusing on genes that have been studied in depthusing mutant analysis. Analyses of these genes have revealed critical players in the basic biologicalprocesses of this unique pathogen, including mycelial growth, appressorium establishment, sclerotialformation, apothecial and ascospore development, and virulence. Additionally, the synthesis hasuncovered gaps in the current knowledge regarding this fungus. We hope that this review will serveto build a better current understanding of the biology of this under-studied notorious soilbornepathogenic fungus.Keywords: soilborne fungal pathogen; Sclerotinia sclerotiorum; fungal pathogenesis; sclerotialformation; apothecial development; fungal growth1. IntroductionAscomycete Sclerotinia sclerotiorum (Lib.) de Bary is a soilborne pathogenic fungus, which wasfirst described as Peziza sclerotiorum by Libert [1]. In 1945, Whetzel [2] established S. sclerotiorum (Lib.)de Bary as the major species of Sclerotinia, as it is the best-known and most economically importantpathogen of the genus. It was proposed as the representative species for the genus Sclerotinia in the1970s [3,4]. The Special Committee on Fungi and Lichens recommended the generic name Sclerotinia,and so did the General Committee of the International Association of Plant Taxonomists later on [5].S. sclerotiorum belongs to the family Sclerotiniaceae [2] of the class Leotiomycetes. Sclerotiniaceaealso includes two other very closely related species, S. minor and S. trifoliorum. All three speciesproduce vegetative resting structures, termed sclerotia, and mushroom-like reproductive structures,named apothecia, during their life cycles. However, S. minor forms small sesame-sized sclerotia,whereas S. sclerotiorum and S. trifoliorum can form large sclerotia as big as peas. They all lack anobvious conidial stage. S. sclerotiorum has the broadest host range, which includes both herbaceousand succulent plants, and even some woody ornamentals and monocots. S. trifoliorum was isolatedPathogens 2020, 9, 27; doi:10.3390/pathogens9010027 www.mdpi.com/journal/pathogensPathogens 2020, 9, 27 2 of 22from vegetable legumes, while S. minor has been found on sunflowers, tomatoes, carrots, peanuts,and lettuce.S. sclerotiorum is a highly damaging pathogen with diverse infection modes and a double feedinglifestyle of both biotroph and necrotroph (Figure 1) [6,7]. It attacks host plants either by means ofascospores that can be discharged forcibly upwards from apothecia into the air, or by myceliumarising from infected tissue or from germinated sclerotia [8]. When ascospores land on susceptiblehost tissue, they can germinate under favorable conditions and start a new cycle of infection. To date,the microconidia of S. sclerotiorum have been observed amongst the mycelium and on the surfacesof sclerotia. However, no evidence of their functionality has been identified. Under moist andcool conditions, this fungus rapidly grows inside the infected host tissues and develops symptomsof browning, water-soaking, and a white, cotton-like mycelium, which leads to necrosis, stunting,premature ripening, and wilting of the host [8]. Therefore, the diseases that it causes have been givennames, including stem rot, drop, crown rot, cottony rot, watery soft rot, blossom blight, and Sclerotiniablight. Upon killing the host, the fungus can saprophytically grow on the dead plant tissue. Sclerotiaare later abundantly formed on the host surface and cavities, in plant debris, and in soil, where theyare able to remain dormant for up to 10 years [9].Pathogens 2020, 9, x FOR PEER REVIEW 2 of 22 and succulent plants, and even some woody ornamentals and monocots. S. trifoliorum was isolated from vegetable legumes, while S. minor has been found on sunflowers, tomatoes, carrots, peanuts, and lettuce. S. sclerotiorum is a highly damaging pathogen with diverse infection modes and a double feeding lifestyl f both biotroph and necrotrop (Figure 1) [6,7]. It attacks host plants either by mea s of ascospores t at can be discharged forcibly upwards from apothecia into the air, or by mycelium arising from infected t sue or from germinated scle tia [8]. When ascospores land on susceptible host tissue, th y can germinate und favorable onditions and start a new cycle of infection. To date, the microconidia of S. sclerotiorum h e been observed amongst he mycelium and on the surfaces of sclerotia. However, no ev dence of their functionality has been identif ed. U er moist and cool conditions, this fungus rap ly grows inside the i fected host tissues and develops symptoms of browning, water-soaking, n a white, cotton-like mycelium, which lea s to necro is, stunting, p emature ripening, and wilting of the host [8]. Th refore, the diseases th t it causes have been given names, including stem rot, drop, crown rot, cottony rot, w t ry soft rot, blossom blight, and Sclerotinia blight. Upon killing the host, he fungus can saprophytically grow on the dead plant tissue. Sclerotia are later abunda tly formed on t e host su face and cavities, in plant debris, and in soil, where they are abl to remain dormant for up to 10 years [9]. Figure 1. Life cycle of Sclerotinia sclerotiorum. S. sclerotiorum has an extremely broad host range, which consists of more than 600 plant species, including almost all dicotyledonous and some monocotyledonous plants [10,11]. It can infect many economically important crops, such as canola; legumes such as soybean and peanut; sunflower; various vegetables such as lettuce and tomato; and monocotyledonous plants such as tulip and onion [10,12]. It is therefore not surprising that it causes significant economic losses globally every year [13]. For example, in China, oilseed rape yield losses that are caused by SSR (Sclerotinia stem rot) usually Figure 1. Life cycle of Sclerotinia sclerotiorum.S. sclerotiorum has an extremely broad host range, which consists of more than 600 plant species,including almost all dicotyledonous and some monocotyledonous plants [10,11]. It can infect manyeconomically important crops, such as canola; legumes such as soybean and peanut; sunflower;various vegetables such as lettuce and tomato; and monocotyledonous plants such as tulip andonion [10,12]. It is therefore not surprising that it causes significant economic losses globally everyyear [13]. For example, in China, oilseed rape yield losses that are caused by SSR (Sclerotinia stemrot) usually range from 10 to 20% and they may be up to 80% for severe SSR outbreak seasons [14–16].In The United States, annual losses that are caused by this pathogen have exceeded $200 million [12].Pathogens 2020, 9, 27 3 of 22As with most other fungal pathogens, chemical control is the most commonly used method forcontrolling the diseases that are caused by S. sclerotiorum, although it is environmentally unfriendlyand can induce resistance from the pathogen. Chemical control also becomes less effective once thesclerotia are formed. Obviously, the incidence of disease would be greatly reduced if sclerotia couldbe either prevented from forming or destroyed in soil and plant debris. Flooding and crop rotationare good options that accelerate the decay of sclerotia [17]. However, flooding is impractical in mostareas, and crop rotation has been found to be less effective as a control measure [18,19], because ofthe long survival periods of sclerotia in soil. Measures, like widening row spacing, and using wiretrellis supports to raise foliage from the ground have been reported to be helpful [18,20]. However,factors, such as type of crop, method of cultivation, and environmental conditions, always affect theeffectiveness of each control method.For major crop diseases, the most welcoming and environmentally friendly control method isthrough the use of resistant cultivars. However, strong host single-gene resistance has not been foundagainst S. sclerotiorum [12], which makes it difficult to improve resistance using classical breedingmethods [7]. Even with mild resistance, the traits seem to be multigenic. Future development ofintegrated approaches may help to control the spread of the fungus with better understanding of thebiology of this notorious pathogen and better QTL mapping strategies.In this review, we focus on recent key molecular findings on the unique biology and pathogenesisprocess of S. sclerotiorum. A brief summary of the genome of the pathogen will also be discussed.The genomic sequences of S. sclerotiorum have been available for less than a decade [21]. However,it was recently updated with higher completion and better gene annotation [22]. We hope that thisreview will serve to build a better current understanding of the biology of this notorious soilbornepathogenic fungus.2. The Features of the S. sclerotiorum Genome2.1. Genome SequencesThe genome of S. sclerotiorum strain 1980, originally isolated from beans in western Nebraska USA,was first sequenced in 2011 using Sanger technology with 9.1x coverage. As approximately 1.6 Mb ofsequences were not covered by the 38.0 Mb scaffolds, and thus missed from the assembly, the final sizeof S. sclerotiorum genome was estimated to be approximately 38.3 Mb, which consists of 16 linkagegroups likely corresponding to 16 chromosomes (GenBank accession numbers: AAGT01000000) [21].Most of the uncovered regions are located in the middle of chromosomes, which probably correspondto centromeres. The genome was predicted to contain 14,522 genes, with average GC contents of 41.8%.After removing genes encoding small proteins that are less than 100 amino acids in length or withoutevidence of expression (from ESTs and/or microarray signals), 11,860 predicted proteins with highconfidence were deduced [21].Initial analyses of the genome sequences revealed a large number of virulence related genes thatwere possessed by the S. sclerotiorum 1980 strain, including genes encoding cell wall degrading enzymes(CWDEs) and biosynthesis genes of phytotoxins and other secondary metabolites [21]. Amselem etal. also identified a significant amount of repetitive transposable elements (TEs), which comprisesapproximately 7.7% of the whole genome. This led to a postulation that the S. sclerotiorum genomeexperienced a recent major remodeling that was associated with a dramatic expansion of TEs. The TEexpansion in S. sclerotiorum might also have an impact on its genome organization and function ofgene inactivation, modification, or expression regulation [21].Derbyshire et al. recently sequenced the genome sequence of the same S. sclerotiorum 1980 strainto near completion in 2017 using PacBio technology. It was annotated using extensive RNA-Seq dataand manual curation. Therefore, this version of the whole-genome sequence became the choice ofstandard for Sclerotinia. They identified 70 candidate effector genes, and found a significant associationbetween the positions of these secreted proteins and regions with a high relative RIP (repeat-inducedPathogens 2020, 9, 27 4 of 22point mutation) index, which suggested that S. sclerotiorum exhibits a subtly enhanced mutation rate ofsecreted proteins in specific genomic compartments as a result of transposition and RIP activity [23].More recently, Derbyshire et al. sequenced the genomes of 25 field isolates of S. sclerotiorum thatwere collected from four different continents—Australia, Africa (north and south), Europe, and NorthAmerica (Canada and the Northern United States). They conducted SNP-based analyses on populationstructure and selective sweeps [24,25]. These 25 isolates can be grouped into two major populations,where population 1 consists of 11 isolates from Canada, the USA, and France, and population 2 includesnine isolates from Australia and one from Morocco. A single candidate selective sweep was identifiedin the Australian and Moroccan group, which covers less than 0.001% of the genome. It is reasonableto speculate that a slow evolution rate and extensive self-fertilization of S. sclerotiorum may have ledto a striking absence of strong selective sweeps, as there is only one gene within this 10 Kb region,which encodes a major facilitator superfamily transporter that was only negligibly expressed at latestages of Brassica napus infection [22]. In support of such genome conservation, S. sclerotiorum strainsfrom even a tropical and a temperate region, although segregated in the populations, still exhibitsimilar genetic structure [26].2.2. Transcriptomic and Secretomic AnalysisThe availability of the high-quality genome sequences facilitated comparative transcriptomicand secretomic analysis of this notorious pathogen, which in turn facilitated biological investigations.Seifbarghi et al. (2017) was able to delineate gene expression patterns that signified transitions betweenpathogenic phases of S. sclerotiorum, namely, host penetration, ramification, and necrotrophic stages,through RNA-Seq analysis focusing on events occurring through the early (1 h) to the middle (48 h)stages of infection. These expression data provide evidence for the occurrence of a brief biotrophicphase soon after host penetration [27].432 proteins were identified in S. sclerotiorum in an interspecies comparative analysis of thepredicted secretomes of S. sclerotiorum and Botrytis cinerea. Among them, 16% of the encoding genesreside in small gene clusters that are distributed over 13 of the 16 predicted chromosomes [28]. Thesecandidate genes provide a reservoir for future reverse genetics analyses to delineate the pathogenesismechanisms in the S. sclerotiorum-host plant interactions.Mutant analysis is paramount to establish a causal relationship between a gene and a studiedbiological process, as omics experiments only provide vague association clues. Hence, the rest of thisreview will summarize all of the genes studied in S. sclerotiorum so far using such convincing mutantanalysis methods. A Venn diagram of the functions of these encoded proteins is provided for readers’overview (Figure 2). We also constructed a chromosomal map for these genes to detect possibleclustering events that are often associated with virulence factors (Figure 3). However, little clusteringis observed, except for genes contributing to mating and melanisation, reflecting the under-studiednature of this fungus.Pathogens 2020, 9, 27 5 of 22Table 1. List of all Sclerotinia sclerotiorum genes studied so far using mutant analysis. The genes are ordered in regards to their chromosomal positions (Figure 3).Gene Code(New)Gene Code(Old)Strains MutantNameGene FullNameMutantTypeMutant PhenotypesSecretionSignalTested Hosts OtherFunctionsReferenceHyphalGrowthSclerotialFormationOxalateProduction VirulenceAppressoriaFormationInduceHostHR/Resistancesscle_01g003850SS1G_02068Ep-1PNA367,Heilongjiang,Chinassvp1Small secretedvirulence-relatedproteinRNAi - NA NA + NA + Yes Canola(Zhongyou 821)HRinduction [30]sscle_01g004990SS1G_019191980,Nebraska,USAsvf1 Survival factor1 homologue RNAi - NA - + + NA NoArabidopsisand canola(Zhongyou 821)Cell wallintegrity,ROSproduction[31]sscle_01g006030SS1G_017881980,Nebraska,USAcna1Catalyticsubunitcalcineurin-encoding geneRNAi + + - + - NA NoArabiposisand tomato(Bonny Best)Hyphalelongation [32]sscle_01g007450SS1G_01614Ep-1PNA367,Heilongjiang,Chinasop1Microbialopsin homologgeneRNAi + + NA + NA NA No Arabidopsis Stressresponses [33]sscle_01g011030SS1G_011511980,Nebraska,USAsfh1GATA-box andSNF5 domainscontainingtranscriptionfactorRNAi + + NA + + NA NoSoybean,common beanand tomatoROSaccumulation [34]sscle_02g013550SS1G_12694HA61,Jiangsu,Chinashk1 Histidinekinases Deletion + + NA - NA NA NoRapeseed,strawberry,tomato andcucumberOxidativestresses,glycerolaccumulation[35]sscle_02g020240SS1G_040031980,Nebraska,USAmat1-1-5 Mating-typegene Deletion - - NA - NA NA No TomatoApothecialdevelopment [29]sscle_02g020250SS1G_040041980,Nebraska,USAmat1-1-1 Mating-typegene Deletion - - NA - NA NA No TomatoApothecialdevelopment [29]sscle_02g020260SS1G_040051980,Nebraska,USAmat1-2-4 Mating-typegene Deletion - - NA - NA NA No TomatoApothecialdevelopment,ascosporeproduction[29]sscle_02g020270SS1G_040061980,Nebraska,USAmat1-2-1 Mating-typegene Deletion + - NA - NA NA No TomatoApothecialdevelopment [29]Pathogens 2020, 9, 27 6 of 22Table 1. Cont.Gene Code(New)Gene Code(Old)Strains MutantNameGene Full Name MutantTypeMutant PhenotypesSecretionSignalTested Hosts OtherFunctionsReferenceHyphalGrowthSclerotialFormationOxalateProduction VirulenceAppressoriaFormationInduceHostHR/Resistancesscle_03g025030SS1G_00699WMA1,Washington,USAsod1 Cu/Zn superoxidedismutase T-DNA - - - + NA NA No Pea (Guido)Detoxificationof host ROS [36]sscle_03g025030SS1G_006991980,Nebraska,USAsod1 Cu/Zn superoxidedismutase Deletion + + + + NA NA NoTomato(GardenPeach) andtobaccoOxidativestresstolerance,repressionof host ROS[37]sscle_03g028510SS1G_00263Isolated froman infectedcanola stem,Alberta,Canadav263 Hypothetical secretedprotein Deletion - NA NA + NA NA Yes Canola [38]sscle_03g031470SS1G_13314Isolated fromdiseasedrapeseed,Alberta,Canadascd1 Scytalone dehydratase Deletion + + NA - NA NA No Rapeseed(Westar)Hyphalbranching [39]sscle_03g031480SS1G_13315Isolated fromdiseasedrapeseed,Alberta,Canadathr1 Trihydroxynaphthalenereductase Deletion + + NA - NA NA NoRapeseed(Westar)Hyphalbranching [39]sscle_03g031520SS1G_133221980,Nebraska,U.S.A.; UF1,Florida;WMA,Washington,USApks13 Polyketide synthaseDeletionbyCRISPR- - NA - + NA NoSoybean,canola,tomato(Better Boy),faba bean(Windsor) andpea (SugarDaddy)Pigmentationofcompoundappressoria[40]sscle_03g031670SS1G_13339274,Nebraska,USApth2 Peroxysomal carnitineacetyl transferase Deletion + + + + + NA No SoybeanOxalic acidaccumulation [41]sscle_04g034810SS1G_02462Isolated froman infectedcanola stem,Alberta,Canadaaxp Arabinofuranosidase/β-xylosidase Deletion NA NA NA + NA NA Yes Canola [42]Pathogens 2020, 9, 27 7 of 22Table 1. Cont.Gene Code(New)Gene Code(Old)Strains MutantNameGene Full Name MutantTypeMutant PhenotypesSecretionSignalTested Hosts OtherFunctionsReferenceHyphalGrowthSclerotialFormationOxalateProduction VirulenceAppressoriaFormationInduceHostHR/Resistancesscle_04g034960SS1G_02486Sunf-M,InnerMongolia,Chinacaf1Secreted protein with aputative Ca2+-bindingEF-hand motifRNAi,T-DNA + + - + + + YesArabidopsis,rapeseed, pakchoi cabbage,hot pepper,tomato,cucumber andsoybean[43]sscle_04g037170SS1G_027841980,Nebraska,USAscat1 Type A catalase Deletion + + NA + NA NA NoTomato(GardenPeach)Modulationof ROS [44]sscle_04g038020SS1G_02904Ep-1PNA367,Heilongjiang,Chinacvnh Secreted protein RNAi + + NA + NA NA Yes Arabidopsis [45]sscle_05g046240SS1G_05917SUN-F-M,InnerMongolia,Chinasl2 Cell wall protein RNAi - + NA - NA NA Yes Rapeseed andArabidopsisCellularintegrity [46]sscle_05g046390SS1G_058991980,Nebraska,USAtrr1 Thioredoxin reductase RNAi NA + NA + NA NA No Arabidopsisand tobaccoOxidativestresstolerance[47]sscle_05g046790SS1G_058391980,Nebraska,USAbi1 Bax inhibitor-1 protein RNAi + - - + NA NA No Arabidopsisand tomatoStressresponses,hyphal tipbranching[48]sscle_05g046830SS1G_05834 JRUF1,Florida, USA foxe2Forkhead-boxtranscription factorfamily geneDeletion,T-DNA - - NA - - NA No TomatoApothecialdevelopment [49]sscle_05g048220SS1G_056611980,Nebraska,USAnox1 NADPH oxidase RNAi - + + + NA NA No Tomato(Rutger)ROSregulation [50]sscle_06g049430SS1G_074041980,Nebraska,USArhs1Rearrangement hot spotrepeat-containingproteinRNAi + + - + + NA YesArabidopsisand canola(Zhongshuang9)[51]sscle_06g049780SS1G_073601980,Nebraska,USAfkh1Atypical forkhead(FKH)-box-containingproteinRNAi + + NA + NA NA No Tomato Cellularintegrity [52]Pathogens 2020, 9, 27 8 of 22Table 1. Cont.Gene Code(New)Gene Code(Old)Strains MutantNameGene Full Name MutantTypeMutant PhenotypesSecretionSignalTested Hosts OtherFunctionsReferenceHyphalGrowthSclerotialFormationOxalateProduction VirulenceAppressoriaFormationInduceHostHR/Resistancesscle_06g049830SS1G_073551980,Nebraska,USApac1 pH-Responsivetranscription factor Deletion - + + + NA NA NoArabidopsisand tomato(Bonnie Best)[53]sscle_06g049890SS1G_07345 NGA4,Anhui, China pemg1Elicitor-homologousprotein RNAi + NA - + + NA NoOilseed rapeand soybeanNegativeregulator ofgrowth andvirulence[54]sscle_06g051560SS1G_07136 UF1, Florida,USA ste12Downstreamtranscription factor ofMAPK pathwayRNAi + + NA + + NA No Bush beanand tomato [13]sscle_07g055970SS1G_03527SUN-F-M,InnerMongolia,Chinahex1 Woronin body majorprotein RNAi - + NA NA NA NA NoCellularintegrity [46]sscle_07g058030SS1G_03252 UF1, Florida,USA ams2Cell-cycle-regulatedGATA transcriptionfactorRNAi + - NA + + NA No CommonbeanChromosomesegregation,numberanddistributionof sclerotia[55]sscle_07g058620SS1G_031711980,Nebraska,USApka1 Protein kinase A Deletion - - - NA NA NA No PKAactivity [56]sscle_07g059700MK9929131980,Nebraska,USAqdo Quercetin dioxygenasegene Deletion - NA NA + NA NA Yes ArabidopsisFlavonoldegradation [57]sscle_08g064670SS1G_051631980,Nebraska,USAcry1 Cryptochrome familyCRY-DASH ortholog Deletion - - NA - NA NA NoArabidopsisand tomatoSclerotialmass,response toUV[58]sscle_08g065550SS1G_05284 NGA4,Anhui, China nacαNascentpolypeptide-associatedcomplex α-subunitRNAi - - - + NA NA No Oilseed rapeand tobacco [59]sscle_08g066770SS1G_054451980,Nebraska,USAsmk3 Slt2 ortholog Deletion + + NA + + NA No Canola(Westar)Cuticlepenetration,cell wallintegrity[60]Pathogens 2020, 9, 27 9 of 22Table 1. Cont.Gene Code(New)Gene Code(Old)Strains MutantNameGene FullNameMutantTypeMutant PhenotypesSecretionSignalTested Hosts OtherFunctionsReferenceHyphalGrowthSclerotialFormationOxalateProduction VirulenceAppressoriaFormationInduceHostHR/Resistancesscle_08g067830SS1G_055881980,Nebraska,U.S.A.mads MADS-boxproteins RNAi + - NA + NA NA No Tomato [61]sscle_08g068500SS1G_14133Ep-1PNA367,Heilongjiang,Chinaitl Integrin-likeprotein RNAi + + NA + NA + YesArabidopsisand canolaHyphalbranching,suppressionof hostdefense[62]sscle_08g068530SS1G_141271980,Nebraska,USAggt1 γ-Glutamyltranspeptidase Deletion - + NA - + NA Yes Tomato [63]sscle_09g069850SS1G_107961980,Nebraska,USAodc2 Oxalatedecarboxylases Deletion - - + + + NA YesCommonbean (BushBlue Lake 47),soybean(Harosoy),tomato(Bonnie Best)and celery[64]sscle_10g075560SS1G_08218WMA1,Washington,USAoah Oxaloacetateacetylhydrolase T-DNA - - + + NA NA NoFaba bean(BroadWindsor), pea(Guido), greenbean (GreatNorth Tara)and soybean(Skylla)[65]sscle_10g075560SS1G_082181980,Nebraska,USAoah1 Oxaloacetateacetylhydrolase Deletion - + + + + NA NoTomato(Bonnie Best),common bean(Bush BlueLake 47),soybean(Harosoy),canola,Arabidopsisand sunflower[66]Pathogens 2020, 9, 27 10 of 22Table 1. Cont.Gene Code(New)Gene Code(Old)Strains MutantNameGene FullNameMutantTypeMutant PhenotypesSecretionSignalTested Hosts OtherFunctionsReferenceHyphalGrowthSclerotialFormationOxalateProduction VirulenceAppressoriaFormationInduceHostHR/Resistancesscle_10g075560SS1G_082181980,Nebraska,U.S.A.; UF1,Florida;WMA,Washington,USAoah1 OxaloacetateacetylhydrolaseDeletionbyCRISPR- + + + + NA NoSoybean,canola,tomato (BetterBoy), fababean(Windsor),and pea(SugarDaddy)[40]sscle_10g077630SS1G_084891980,Nebraska,USApph1Type 2ASer/Thrphosphatasecatalyticsubunit PP2AcRNAi + + NA NA NA NA No [67]sscle_10g079320SS1G_140651980,Nebraska,USAssp1 Development-specific protein Deletion - - NA NA NA NA NoResistancetoglycoside-containingantibiotics[68]sscle_11g082700SS1G_078711980,Nebraska,USArgb1Type 2ASer/Thrphosphatase BsubunitRNAi - + NA + + NA NoArabidopsisand tomato(Bonny Best)MAPKpathway [67]sscle_11g083230SS1G_07798SUN-F-M,InnerMongolia,Chinagpdglyceraldehyde-3-phosphatedehydrogenaseRNAi NA + NA NA NA NA No [46]sscle_11g083680SS1G_077491980,Nebraska,USAxyl1 Endo-β-1,4-xylanase Deletion + + NA + NA NA YesCanola andArabidopsisApotheciaformation [69]sscle_11g083950SS1G_077151980,Nebraska,USAsac1 Adenylatecyclase Deletion + + - + NA NA NoTomato(Bonnie Best)Apotheciaproduction,cAMP-signaling[70]sscle_12g087830SS1G_111721980,Nebraska,USAnox2 NADPHoxidase RNAi - + - - NA NA NoTomato(Rutger)ROSregulation [50]sscle_12g090900SS1G_118661980,Nebraska,USAsmk1 ERK -typeMAP kinase RNAi + + NA NA NA NA NopH-dependentregulation [71]Pathogens 2020, 9, 27 11 of 22Table 1. Cont.Gene Code(New)Gene Code(Old)Strains MutantNameGene FullNameMutantTypeMutant PhenotypesSecretionSignalTested Hosts OtherFunctionsReferenceHyphalGrowthSclerotialFormationOxalateProduction VirulenceAppressoriaFormationInduceHostHR/Resistancesscle_14g099710SS1G_088141980,Nebraska,USAodc1 Oxalatedecarboxylases Deletion - NA NA - NA NA YesCommonbean (BushBlue Lake 47),soybean(Harosoy) andtomato(Bonnie Best)[64]sscle_16g107670SS1G_100961980,Nebraska,USAcp1 Cerato-plataninprotein Deletion - - NA + NA + YesArabidopsisand tobaccoInteractionwith PR1 [72]sscle_16g107670SS1G_10096 FXGD2,Anhui, China sm1Cerato-plataninprotein RNAi + + - + NA NA YesTobacco,oilseed rapeand soybean[73]sscle_16g107930SS1G_101351980,Nebraska,USAfdh1 Formaldehydedehydrogenase Deletion - + NA + + NA NoCommonbean andtomatoOsmoticoxidativestressresistance[74]sscle_16g109570ANQ804471980,Nebraska,USAnsd1GATA-type Ivbzinc-fingertranscriptionfactorDeletion - - NA + + NA NoTomato(Bonnie Best),celery andtomatoAscogoniaformation,apotheciumdevelopment[75]The assembly genome for the new version gene code is ASM185786v1 published in 2017 and ASM14694v1 for the old version published in 2011. ‘+’ in the table represents that thecorresponding phenotype of mutant is altered compared to wild type strain, while ‘-’ means that the phenotype remains unchanged. NA means not assessed. The secretion signals werefound using ‘SignalP-5.0’. Unless specified, all deletions were generated with homologous recombination. The Latin names of host species used for pathogenicity test of mutants are:Apium graveolens (celery), Arabidopsis thaliana (Arabidopsis), Brassica napus (canola, oilseed rape, rapeseed), Brassica rapa subsp. chinensis (pak choi cabbage), Capsicum frutescens (hotpepper), Cucumis sativus (cucumber), Fragaria ananassa (strawberry), Glycine max (soybean), Helianthus annuus (sunflower), Lycopersicon solanum (tomato), Nicotiana benthamiana (tobacco),Phaseolus vulgaris (bush bean, common bean, green bean), Pisum sativum (pea), Vicia faba (faba bean). The ecotype of A. thaliana mentioned in the table is Columbia-0. The specific localcultivars of host species are shown in brackets.Pathogens 2020, 9, 27 12 of 22Pathogens 2020, 9, x FOR PEER REVIEW 5 of 22 Figure 2. A Venn diagram summary of the genes that have been studies with mutant analysis (detailed in Table 1). Figure 2. A Venn diagram summary of the genes that have been studies with mutant analysis (detailedin Table 1).Pathogens 2020, 9, 27 13 of 22Pathogens 2020, 9, x FOR PEER REVIEW 6 of 22 Figure 3. Map positions of the genes in Table 1. The numbers on the left of each chromosome represent the locations of these genes. Genes labelled in green are involved in the development of S. sclerotiorum, including hyphal growth, sclerotial formation, apothecial formation and etc. Genes labelled in red mainly play roles in virulence of S. sclerotiorum. Genes labelled in blue are involved in both while the ones labelled in black are involved in other biological processes. The chromosomal map was drawn using ‘MapChart’ software. 3. Molecular Dissection of S. sclerotiorum Biology Here we adopt the gene/mutant/protein nomenclature that is most commonly used by Sclerotinia researchers, as there are many discrepancies in S. sclerotiorum literature. As an example, Abc1 protein is encoded by wild-type gene that is italicized as Abc1. Mutant is denoted as abc1. Exceptions are specifically explained. Another consideration to keep in mind is the presence of huge variations in the field isolates and local hosts used in these studies (Table 1), which likely contribute to some of the discrepancies that were observed in the phenotypes of mutants of the same genes. 3.1. Regulation of Mycelial Growth and Virulence During the last two decades, the availability of whole genome sequences and improved transformation as well as knockdown/knockout methods have greatly facilitated the molecular study of S. sclerotiorum. Most of the genes studied so far that affect growth are relatively conserved genes that also affect differentiation, such as sclerotial and apothecial development (Figure 2), which will be discussed in the next sections. In this part, we specifically discuss genes only affecting hyphal growth rate and virulence, but not differentiation, during development, as mycelial growth precedes processes of virulence and differentiation. It is not surprising that the mutants here with major growth defects often exhibit virulence attenuation, although there are certainly exceptions such as mat1-2-1, which exhibits slower growth, aberrant apothecial morphogenesis, but normal virulence [29] (discussed more later). Figure 3. Map positions of the genes in Table 1. The numbers on the left of each chromosome representthe locations of these genes. Genes labelled in green are involved in the development of S. sclerotiorum,including hyphal growth, sclerotial formation, apothecial formation and etc. Genes labelled in redmainly play roles in virulence of S. sclerotiorum. Genes labelled in blue are involved in both while theones labelled in black are involved in other biological processes. The chromosomal map was drawnusing ‘MapChart’ software.3. Molecular Dissection of S. sclerotiorum BiologyH re we adopt he gene/mutant/protein n menclature that is most commonly used by Sclerotiniaresearchers, as there are many discrepancies in S. sclerotiorum literature. As an example, Abc1 proteinis encoded by wild-type gene that is italicized as Abc1. Mutant is denoted as abc1. Exceptions arespecifically explained. Another consideration to keep in mind is the presence of huge variations inthe field isolates and local hosts used in these studies (Table 1), which likely contribute to some of thediscrepancies that were observed in the phenotypes of mutants of the same genes.3.1. Regulation of Mycelial Growth and VirulenceDuring the last two decades, the availability of whole genome sequences and improvedtransformation as well as knockdown/knockout methods have greatly facilitated the molecularstudy of S. sclerotiorum. Most of the genes studied so far that affect growth are relatively conservedgenes that also affect differentiation, such as sclerotial and apothecial development (Figure 2), which willbe discussed in the next sections. In this part, we specifically discuss genes only affecting hyphalgrowth rate and virulence, but not differentiation, during development, as mycelial growth precedesprocesses of virulence and differentiation.It is not surprising that the mutants here with major growth defects often exhibit virulenceattenuation, although there are certainly exceptions such as mat1-2-1, which exhibits slower growth,aberrant apothecial morphogenesis, but normal virulence [29] (discussed more later).The RNAi knockdown of highly conserved transcription factors Ams2 or Mads lead to reducedmycelial growth rate and virulence, which suggested that they are early growth regulators. Ams2 is aPathogens 2020, 9, 27 14 of 22GATA-box domain transcription factor. Ams2 is required for proper expression of histone and cell cyclerelated genes, similar as in Schizosaccharomyces pombe [55]. Mads is orthologous to yeast Mcm1 with aMADS-box domain, which is essential for viability, cell cycle, mating, mini-chromosome maintenance,recombination, and stress tolerance [61]. Although mutants of these early growth factors severelyaffect growth, they can still form sclerotia, which indicated that the later stages of fungal differentiationpathways, such as sclerotial formation and apothecial development, might be less dependent on theseearly growth factors.BAX inhibitor-1 (Bi1) is a highly conserved protein that is found in both eukaryotes and prokaryotes,exhibiting apoptosis-inhibiting activity. RNAi knockdown mutants in S. sclerotiorum showed moreaerial hyphal growth and reduced virulence [48]. The mutants also exhibit reduced tolerance tochemical stress, as its gene expression is induced by various stresses. Bi1 is likely a stress specificregulator dedicated to both biotic and abiotic stress responses, due to its minor roles in growthand development.Unlike the previously described genes, PemG1 serves an opposite function in regards to growthand virulence. The RNAi mutants of PemG1 exhibit faster mycelial growth and enhanced virulence,indicating that it is a negative regulator in these processes. Consistently, more infection cushions,more CWDE activities, and less susceptibility to salt stress were observed [54]. However, the exactmechanism on how this fungal specific protein negatively regulates growth and virulence is unclear.3.2. Signaling Events Leading to Sclerotial FormationSclerotia of S. sclerotiorum initiate with small primordia and rapidly develop into whitecompact hyphal masses. They mature with dehydration and pigmentation once they cease growth.The melanised outer surface of the sclerotium is mostly responsible for resisting adverse conditions [8].We will first discuss the genes affecting both growth and sclerotial formation, which are likelyvery upstream components that are shared by both processes. As expected for broad regulators,these mutants show not only defective growth and sclerotial malformation, but also almost alwaysloss of virulence and other pleiotropic defects (Table 1).The melanisation of sclerotia is an important process for the long-term survival of Sclerotiniaspecies in nature. The deletion of melanin biosynthesis genes scytalone dehydratase (Scd1) ortrihydroxynaphthalene reductase (Thr1) resulted in slower mycelial growth, reduced number, size, andpigmentation of sclerotia [39], which suggested that melanisation is critical for sclerotial maturationand perhaps feedback promotion of growth. However, unlike in other pathogenic fungi, the virulenceof these knockout strains is not affected, suggesting that melanin does not contribute to pathogenesisin Sclerotinia as it does for other fungi, like Magnaporthe species.Knocking out some other conserved genes in S. sclerotiorum can also lead to diverse defects. Forexample, the peroxisomal carnitine acetyl transferase (CAT) encoding gene in S. sclerotiorum is Pth2.The CAT activity is required for acetyl-CoA transport, which is needed for fatty acid metabolism. Thepth2 knockout mutants show aberrant growth, non-sclerotial formation, and reduced oxalic acid (OA)levels and virulence [41]. In another instance, the silencing of integrin-like gene Itl leads to alteredcolony morphology, smaller and irregular shaped sclerotia, and hypovirulence [62]. Although Cvnhhomologs seem to only exist in Sclerotinia and Botrytis, the CVNH domain is a conserved domain. Thesilencing of this gene lead to reduced growth rate, non-sclerotial formation and lower virulence [45].Phosphorylation and de-phosphorylation events are critical for almost all signal transductions.Therefore, it is not surprising that a number of kinases and phosphatases are involved in both growthand sclerotial formation. Mutation of two-component histidine kinase Shk1 leads to slower and alteredhyphal growth and failed sclerotial formation [35]. Although the mutant is also sensitive to osmoticstress and shows heightened resistance to fungicides, it exhibits normal virulence. Shk1 likely worksupstream of the MAPK cascade to control these processes. Smk1 and Smk3 are two MAPK kinases thathave been studied in S. sclerotiorum so far. Mutants of these two kinases show similar growth defectsand non-sclerotial formation [60,71], suggesting that they may function downstream of Shk1.Pathogens 2020, 9, 27 15 of 22cAMP could act upstream of the MAPKs, as exogenous application of cAMP inhibits Smk1expression and MAPK phosphorylation [71]. Type 2A phosphoprotein phosphatase Pph1 possiblyfunctions downstream of the MAPK. The mutants of pph1 show arrested growth [67]. Consistently,PP2A R2 B regulatory subunit rgb1 mutants show aberrant sclerotial formation and failed penetrationduring infection [67].Reactive oxygen species (ROS) play diverse roles in development and virulence in fungi. This issupported by the mutant analysis of type I catalase Scat1. The deletion of Scat1 lead to slower radialgrowth, higher number of small sclerotia that are not properly melanised, and hypovirulence [44].Calcium is another common factor that is involved in signaling. The study of Cna1 and Caf1 supportsits contribution in S. sclerotiorum biology. Calcineurin Ser/Thr protein phosphatase Cna1 is conservedin eukaryotes, whose activity is dependent on calcium and calmodulin. Antisense cna1 mutants showaltered growth, sclerotial development, and hypovirulence [32]. Caf1 is a secreted protein with aputative Ca2+-binding EF-hand motif, which seems to be conserved in fungi. caf1 T-DNA mutantsexhibit slightly slower growth, deformed sclerotia, and hypovirulence [43].Conserved transcription factors are another large group of genes that are responsible for signaling.Sfh1 is a GATA transcription factor, but with an SNF5 domain. It is a member of the housekeepingRSC (Remodels Structure of Chromatin) complex, which is an ATP-dependent chromatin remodelerthat is essential for cell cycle [34]. Its diverse functions explain its involvement in growth, sclerotialdevelopment, and virulence. Transcription factor Ste12 likely acts downstream of the MAP kinasecascades. In ste12 RNAi lines, slow growth, smaller sclerotia, and fewer appressoria, leading tohypovirulence, were observed [13]. Forkhead (FKH) box (FOX) family transcription factors areimportant regulators of primary metabolism, cell cycle, and morphogenesis in animals and fungi. fkh1RNAi mutants show slower growth, non-sclerotial formation, hypovirulence, and defective stressresponses [52], suggesting that it is a transcriptional regulator that is shared by multiple pathways.CWDEs have been speculated to play key roles in fungal pathogenesis. In support of this,the deletion of Xyl1 that encoded an endo-β-1, 4-xylanase leads to a loss of pathogenicity. Interesting,growth retardation, less sclerotial formation, and dense hyphal branching were also observed in themutant [69], suggestive of a role of xylanase in development as well.Opsins are conserved light-sensitive proteins involved in circadian rhythms. sop1 RNAi linesshow reduced growth, non-sclerotial formation, hypovirulence, and heightened sensitivities to osmoticand fungicide stresses [33]. These observations suggest that light may have diverse roles in variousprocesses in Sclerotinia through opsins.Rearrangement hotspot (Rhs) repeat-containing proteins are widely distributed in bacteria andeukaryotes. Rhs1 is a secreted protein and its orthologs seem to only be present in Sclerotinia and Botrytisspecies. Rhs1 RNAi mutants show slightly slower colony growth, fewer and larger sclerotial formation,and hypovirulence [51]. These data suggest that Rhs1is likely a key virulence factor for Sclerotiniaand it also slightly contributes to growth and sclerotial development. Cerato-platanins are fungalsecreted elicitors that can trigger plant immunity and cell death. Sm1 can cause host hypersensitiveresponse. Interestingly, besides virulence, RNAi mutants of Sm1 also exhibit slower growth, impairedsclerotial development, and heightened sensitivities to different stresses [73], suggesting a broader roleof the elicitor. However, these defects were not detected in a separate study in deletion mutant cp1mutating the same gene [72]. Future careful transgenic complementation experiments are needed tosolve these discrepancies.The existence of mutants that have normal mycelial growth, but do not form sclerotia, suggestthat later stages of sclerotial development are separated from growth. Although most of thesemutants still show attenuated virulence, some exhibit normal pathogenicity, such as sl2 and ggt1(7-glutamyl transpeptidase). RNAi knockdown of either Sl2, GAPDH (Gpd), or Hex1 lead to alteredsclerotial formation or melanisation, similar to its interacting proteins glyceraldehyde-3-phosphatedehydrogenase (GAPDH) and Hex [46]. However, the virulence of sl2 is not affected, suggesting thatsclerotial formation and virulence can be separately controlled by distinct downstream factors. As aPathogens 2020, 9, 27 16 of 22fungal specific secreted protein localizing to fungal cell wall, how Sl2 affects sclerotial developmentis unclear. Ggt is a highly conserved enzyme that contributes to redox homeostasis. The deletionmutants of ggt1 show much higher GSH+GSSG and hydrogen peroxide accumulation, and separationof the cortex layer of mature sclerotia from the medulla [63]. In addition, the mutants are defective incompound appressoria production, only affecting the penetration stage of infection. These mutantphenotypes suggest that GSH, GSSG, or GSH/GSSG ratio contribute to the regulation of sclerotiamaturation and appressoria development.The rest of the genes studied so far that affect sclerotial formation, but not growth, all showattenuated virulence. They likely act upstream of Sl2 and Ggt. ROS increase was observed in sclerotialinitials and infection cushions in S. sclerotiorum, likely due to the combined activities of NADPHoxidases Nox1 and Nox2. Similar to exogenous application of NADPH inhibitor or ROS scavenger,the RNAi mutants of either Nox1 or Nox2 exhibit failed sclerotial development [50], indicating thatROS is required for sclerotial initiation. Interestingly, reduced OA production and virulence was onlyobserved in nox1, but not nox2, which suggests that these two genes are not fully redundant, likely dueto their different expression patterns. Consistently, when the thioredoxin reductase (Trr1) gene that ispartly responsible for ROS detoxification is silenced, less and larger sclerotia are formed [47]. However,virulence is attenuated in Trr1 silenced strains, suggesting that an optimum ROS is needed for virulence.Low pH was known to promote sclerotial proliferation. The pH-sensitive transcription factorPac1 is responsible for ambient pH-induced gene expression. Consistently, the deletion of Pac1 causedaberrant sclerotial formation and reduced OA levels, thus leading to hypovirulence [53]. As higherlevels of OA reduce pH and may affect ROS homeostasis, proper balance among ROS, OA, and pH islikely paramount for the biology of this fungal pathogen.3.3. Control of Apothecial and Ascospore DevelopmentThe apothecium consisting of a stalk (stipe) and a saucer-shaped disc is characteristic of theSclerotinia genus (Figure 1). Asci develop on the upper surface of apothecia and when they mature,the ascospores are dispersed [8]. As mating-type (Mat) genes have generally been established askey regulators of sexual development of ascomycetes, it is not surprising that they affect apothecialdevelopment in the homothallic S. sclerotiorum. Similar to other fungi, the S. sclerotiorum Mat locuscontains a cluster of four Mat genes encoding transcription factors, with MAT1-1s encoding analpha-domain and Mat1-2s encoding high mobility group (HMG) proteins. By deletion knockoutanalysis [29], each of the four Mat genes were analyzed in regards to their contributions to regularmycelial growth, virulence, sclerotial formation, and apothecial development. While these Matscontribute little to vegetative growth, development, and pathogenesis, Mat1-1-5, Mat1-1-1, andMat1-2-1are essential for early, and Mat1-2-4 is critical for late sexual stages, including apothecial initiation andascospore development. As transcription factors, it is also not surprising that these Mat gene mutantsexhibit altered expression of the Mat locus and putative pheromone and pheromone receptor genes,explaining their potential regulatory mechanism and specific phenotypes.Similar to the Mats, another gene that specifically contributes to apothecial development isFoxE2 [49]. FoxE2 is a member of the forkhead box (FOX) transcription factor (TF) family. FOX proteinsplay diverse roles in morphogenesis, development, pathogenicity, and stress responses in animals andfungi. Knockout analysis of FoxE2 in S. sclerotiorum showed that it does not affect mycelial growth,sclerotial formation, or virulence. The striking mutant phenotypic similarity between the Mats andFoxE2 brings the question on the relationship among these transcription factors. It could be possiblethat a transcriptional network that includes these transcription factors needs to be orchestrated forproper sexual stage development in S. sclerotiorum.As a UV-A photoreceptor, Cry1 was suspected to be involved in apothecial development, as itsexpression was induced by UV during this specific developmental phase. However, no obvious defectsin apothecial development were detected in the cry1 deletion mutant [58], suggesting that it is not amajor regulator, or there exists redundancy masking its effects on photomorphogenesis.Pathogens 2020, 9, 27 17 of 22All other mutants in the literature with defects in apothecial development show pleiotropic defects,including sac1 (Adenylate cyclase) [70] and nsd1 (GATA-type IVb zinc-finger transcription factor) [75],both encoding conserved proteins. cAMP is a well-known molecule with diverse roles for manybiological processes in plant fungal pathogens. Although protein kinase A catalytic subunit gene (Pka1)was hypothesized to mediate cAMP signaling, the pka1 single mutant exhibits non-detectable defects,likely due to genetic redundancy of Pka2 [56]. In comparison, with dramatic cAMP level reduction, thesac1 mutant displays slower growth, abolished pathogenicity, and failed apothecial development [70].In other fungi, Nsd1 serves as transcription factor for development and environmental responses.In nsd1 knockout mutants, altered hyphal growth, smaller sclerotia, failed appressorium formationleading to failed pathogenicity, and failed apothecial initiation were observed [75]. These indicate thatNsd1 is likely a general transcription factor that regulates many processes in S. sclerotiorum, or a specificregulator that regulates a general downstream factor that is shared by many pathways. Recently, theNO homeostasis regulating glutathione-dependent formaldehyde dehydrogenases (Fdh1) encodinggene was revealed to be one of the targets of Nsd1 [74]. The deletion mutants of fdh1 exhibit slowermycelial growth, smaller sclerotia, and defective compound appressoria, leading to failed penetrationinto host tissue, being suggestive of the keys roles NO plays in these processes. The high similaritybetween the fdh1 and nsd1 mutant phenotypes indicates that Fdh1 could be the main target of Nsd1during growth and development.3.4. Regulation of Fungal Pathogenesis of the FungusFollowing a short biotrophic phase after infection, S. sclerotiorum causes tissue maceration andnecrosis leading to rapid cell death and host cell wall degradation during fungus colonization. Toxinsand CWDEs are believed to play critical roles in promoting these processes. The study of axp mutantsdeleting a secreted arabinofuranosidase/β-xylosidase precursor reflects the importance of CWDEsin the virulence of S. sclerotiorum. Attenuated virulence was observed in canola. Similarly, thecritical contribution of ROS in virulence is corroborated in sod1 mutants affecting Cu/Zn superoxidedismutase [36,37]. OA is another key factor that has long been hypothesized to contribute to thepathogenicity of this pathogen. Readers are referred to two excellent reviews that have summarizedthe historic and comprehensive studies of the pathogenicity and virulence of S. sclerotiorum [65,66].During infection, S. sclerotiorum produces large amounts of OA. Earlier physiological andpharmacological studies have highlighted its importance. In addition to virulence, UV mutantswhere the exact mutations were not identified could not produce OA and failed to form sclerotia [76],also suggesting a link between OA and development. It was not until the availability of geneticallydefined OA deficient mutants that the contribution of OA towards Sclerotinia biology was partly settled.In odc2 RNAi strain where the gene encoding oxalate decarboxylase in charge of catabolism of OA issilenced, less and non-functional appressoria were formed, leading to hypovirulence [64]. These datasupport the involvement of developmentally regulated OA accumulation in penetration-dependentinfection. In recently generated oah (oxaloacetate acetylhydrolase) mutants through the deletionor CRISPR, where OA biosynthesis is blocked, failed appresorium formation, hypovirulence, anddelayed sclerotial formation was observed [40]. However, the deletion or T-DNA mutants of oahin a separate study show pH-dependent virulence alteration and normal growth and development.These discrepancies can likely be resolved through more careful examination of other mutants that aredeficient in OA biosynthesis.Many pathogen effectors are secreted into the host to dampen host immunity and/or promotevirulence. In recent years, effector biology has been focusing on the study of secreted proteins, as theseeffector candidates can be relatively easily identified through secretome and RNA-seq analysis. Manysecreted proteins in S. sclerotiorum have diverse roles in both development and virulence (Table 1 anddiscussions in the previous sections). Examples of effectors only affecting virulence in S. sclerotioruminclude Ssvp1, V263 and Qdo (quercetin dioxygenase). Less conserved Ssvp1 [30] and V263 [38]are both small secreted proteins that contribute to virulence. On the other hand, more conservedPathogens 2020, 9, 27 18 of 22Qdo catalyzes the cleavage of the flavonol carbon skeleton [57], revealing the critical contributions ofdegrading host anti-microbial flavonol in fungal virulence.Besides secreted proteins, there are also non-secreted regulators that are solely dedicated topathogen penetration and virulence regulation. The examples in S. sclerotiorum include Svf1 (Survivalfactor 1) [31], Pks13 (polyketide synthase 13) [40], and Nacα (nascent-polypeptide-associated complexalpha subunit) [59]. In yeast, Svf1 promotes survival under oxidative stress conditions. Therefore, itlikely assists in coping with ROS during infection in Sclerotinia. Pks13 is likely involved in melaninbiosynthesis in appressoria, as its CRISPR mutant exhibits albino compound appressoria withoutaffecting virulence. Nacα is a highly conserved protein with transcriptional co-activator activity.Interesting, Nacα negatively impacts the expression of polygalacturonase-encoding genes, which likelycontributes to the enhanced virulence phenotypes of the mutant.4. Summary and Future PerspectivesOver the decade, many genes that have been involved in pathogen development and pathogenesishave been characterized in S. sclerotiorum (Table 1). Much has been unveiled for the pathogen growth,development, and differentiation signaling pathways. Accordingly, more evidence is supporting thetwo-phase infection model, where the pathogen suppresses host basal defense prior to killing anddegrading host cells [11]. In the short biotrophic phase, the pathogen uses well-orchestrated strategiesto overcome host immunity. It might spatially achieve this via the production of OA, ROS, CWDEs,and effectors in compound appressoria or primary invasive hyphae.Among almost 15,000 genes encoded in its genome, less than 60 have been studied so far usingcareful mutant analysis. This explains the under-studied nature of this notorious pathogen and thelack of connections in the signaling pathways of its different special biological processes. Besides thetraditional one-gene-at-a-time reverse genetics analysis, more robust methods, such as genome-wideCRISPR, should be developed to enhance the study of this economically important fungus.Due to the short biotrophic period, as well as the switching to necrotrophic phase, identifying andassigning the temporal, spatial, and tissue-specific functions to virulence factors are real challenges.Future development of cell biology and biochemical tools tailored for S. sclerotiorum will offeropportunities for solving many mysteries of the fungus. Considering this specific form of pathogen-hostinteraction system, challenges also exist ahead in applying quantitative disease resistance breeding andphenotypic screens for stage-specific defenses. More collaboration among the molecular pathologistsand breeders will be critical to solve the host resistance difficulties of the pathogen.Author Contributions: S.X., Y.X. and X.L. wrote the review. Y.X. made Table 1 and Figure 3. R.H. made Figure 1,and J.Z. made Figure 2. Y.X. and L.Q. collected references. All authors have read and agreed to the publishedversion of the manuscript.Funding: National Natural Science Foundation of China (Grants 31971836) and Scientific Research Fund ofHunan Provincial Education Department (Grants 17A095) to SX; Canadian foundation of Innovation (CFI),NSERC-Discovery and NSERC-CREATE-PRoTECT funds to XL. YX is partly supported by a scholarship fromChina Scholarship Council (CSC).Acknowledgments: The authors would like to apologize for works that are not cited due to space limitations.We greatly appreciate the constructive suggestions from the three anonymous reviewers, which helped us improvethe quality of this review. We would like to thank National Natural Science Foundation of China (Grants 31971836)and Scientific Research Fund of Hunan Provincial Education Department (Grants 17A095) for funds to S.X.,and Canadian foundation of Innovation (CFI), NSERC-Discovery and NSERC-CREATE-PRoTECT programs forfinancial supports to X.L. Y.X. is partly supported by a scholarship from China Scholarship Council (CSC).Conflicts of Interest: The authors declare no conflict of interests.References1. Libert, M.A. Plante Crytogamicae Arduennae (Exsiccati); 1837; No. 326; Published by the Author.2. Whetzel, H.H. A synopsis of the genera and species of the Sclerotiniaceae, a family of stromatic inoperculatediscomycetes. Mycologia 1945, 37, 648–714. [CrossRef]Pathogens 2020, 9, 27 19 of 223. Buchwald, N.F.; Neergaard, P.J. A plea for the retention of Sclerotinia sclerotiorum as type species for the genusSclerotinia Fckl. emend. Friesia 1972, 10, 96–99.4. Buchwald, N.F.; Neergaard, P.J. Proposal to conserve Sclerotinia Fckl, with S. Sclerotiorum (Lib.) de bary astype species. Taxon 1976, 25, 199–200. [CrossRef]5. Kohn, L.M. Delimitation of the economically important plant pathogenic Sclerotinia species. Phytopathology1979, 69, 881–886. [CrossRef]6. Kabbage, M.; Yarden, O.; Dickman, M.B. Pathogenic attributes of Sclerotinia sclerotiorum: Switching from abiotrophic to necrotrophic Lifestyle. Plant Sci. 2015, 233, 53–60. [CrossRef] [PubMed]7. Wang, Z.; Bao, L.L.; Zhao, F.Y.; Tang, M.Q.; Chen, T.; Li, Y.; Wang, B.X.; Fu, B.; Fang, H.; Li, G.Y.; et al.BnaMPK3 is a key regulator of defense responses to the devastating plant pathogen Sclerotinia sclerotiorum inoilseed rape. Front. Plant Sci. 2019, 10, 1–18. [CrossRef] [PubMed]8. Willetts, H.; Wong, J.J. The biology of Sclerotinia sclerotiorum, S. Trifoliorum, and S. Minor with emphasis onspecific nomenclature. Bot. Rev. 1980, 46, 101–165. [CrossRef]9. Harper, G.E.; Frampton, C.M.; Stewart, A. Factors influencing survival of sclerotia of Sclerotium cepivorum inNew Zealand soils. N. Z. J. Crop Hortic. Sci. 2002, 30, 29–35. [CrossRef]10. Boland, G.J.; Hall, R. Index of plant hosts of Sclerotinia sclerotiorum. Plant Sci. 1994, 16, 93–108. [CrossRef]11. Liang, X.; Rollins, J.A. Mechanisms of broad host range necrotrophic pathogenesis in Sclerotinia sclerotiorum.Phytopathology 2018, 108, 1128–1140. [CrossRef]12. Bolton, M.D.; Thomma, B.P.H.J.; Nelson, B.D. Sclerotinia sclerotiorum (Lib.) de Bary: Biology and moleculartraits of a cosmopolitan pathogen. Mol. Plant Pathol. 2006, 7, 1–16. [CrossRef] [PubMed]13. Xu, T.; Li, J.; Yu, B.; Liu, L.; Zhang, X.; Liu, J.; Montes, H.M. Transcription factor SsSte12 was involved inmycelium growth and development in Sclerotinia sclerotiorum. Front. Microbiol. 2018, 9, 1–13. [CrossRef][PubMed]14. Mei, J.; Qian, L.; Disi, J.O.; Yang, X.; Li, Q.; Li, J.; Frauen, M.; Cai, D.; Qian, W. Identification of resistantsources against Sclerotinia sclerotiorum in brassica species with emphasis on B. Oleracea. Euphytica 2011, 177,393–399. [CrossRef]15. Li, G.Q.; Huang, H.C.; Miao, H.J.; Erickson, R.S.; Jiang, D.H.; Xiao, Y.N. Biological control of Sclerotiniadiseases of rapeseed by aerial applications of the mycoparasite Coniothyrium minitans. Eur. J. Plant Pathol.2006, 114, 345–355. [CrossRef]16. Yang, S.J. An investigation on the host range and some ecological aspects on the Sclerotinia disease of theRape plant. Acta Phytopathol. Sin. 1959, 5, 111–122.17. Moore, W.J. Flooding as a means of destroying the sclerotia of Sclerotinia sclerotiorum. Phytopathology 1949, 39,920–927.18. Schwartz, H.; Steadman, J.J. Factors affecting sclerotium populations of, and apothecium production by,Sclerotinia sclerotiorum. Phytopathology 1978, 68, 383–388. [CrossRef]19. Stoner, W.N.; Moore, W.D. Lowland rice farming, a possible cultural control for Sclerotinia sclerotiorum in theEverglades. Plant Dis. Rep. 1953, 37, 181–186.20. Coyne, D.; Steadman, J.; Anderson, F.J. Effect of modified plant architecture of great northern dry beanvarieties (Phaseolus vulgaris) on white mold severity, and components of yield. Plant Dis. Rep. 1974, 58,379–382.21. Amselem, J.; Cuomo, C.A.; Van Kan, J.A.; Viaud, M.; Benito, E.P.; Couloux, A.; Coutinho, P.M.; De Vries, R.P.;Dyer, P.S.; Fillinger, S.; et al. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorumand Botrytis cinerea. PLoS Genet. 2011, 7, e1002230. [CrossRef]22. Charles, M.; Id, D.; Denton-giles, M.; Id, J.K.H.; Chang, S. A whole genome scan of SNP data suggests a lackof abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotiniasclerotiorum. PLoS ONE 2019, 14, e0214201.23. Derbyshire, M.; Denton-giles, M.; Hegedus, D.; Seifbarghi, S.; Rollins, J.; Van, J.; Seidl, M.F.; Faino, L.;Mbengue, M.; Navaud, O.; et al. The complete genome sequence of the phytopathogenic fungus Sclerotiniasclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol. Evol.2017, 9, 593–618. [CrossRef] [PubMed]24. Hermisson, J.; Pennings, P.S. Soft sweeps: Molecular population genetics of adaptation from standing geneticvariation. Genetics 2005, 169, 2335–2352. [CrossRef] [PubMed]Pathogens 2020, 9, 27 20 of 2225. Messer, P.W.; Petrov, D.A. Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol. Evol.2013, 28, 659–669. [CrossRef] [PubMed]26. Del Ponte, E.M.; Eduardo, S.; Lehner, M.S.; Ju, T.J.D.P.; Mizubuti, G.; Pethybridge, S.J. Independently foundedpopulations of Sclerotinia sclerotiorum from a tropical and a temperate region have similar genetic structure.PLoS ONE 2017, 12, e0173915.27. Seifbarghi, S.; Borhan, M.H.; Wei, Y.; Coutu, C.; Robinson, S.J.; Hegedus, D.D. Changes in the Sclerotiniasclerotiorum transcriptome during infection of Brassica napus. BMC Genom. 2017, 18, 266. [CrossRef]28. Heard, S.; Brown, N.A.; Hammond-kosack, K. An interspecies comparative analysis of the predictedsecretomes of the necrotrophic plant pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS ONE 2015,10, e0130534. [CrossRef]29. Doughan, B.; Rollins, J.A.; Avery, S.V. Characterization of MAT gene functions in the life cycle of Sclerotiniasclerotiorum reveals a lineage-specific MAT gene functioning in apothecium morphogenesis. Fungal Biol.2016, 120, 1105–1117. [CrossRef]30. Lyu, X.; Shen, C.; Fu, Y.; Xie, J.; Jiang, D.; Li, G.; Cheng, J. A small secreted virulence-related protein isessential for the necrotrophic interactions of Sclerotinia sclerotiorum with its host plants. PLoS Pathog. 2016,12, e1005435. [CrossRef]31. Yu, Y.; Du, J.; Wang, Y.; Zhang, M.; Huang, Z.; Cai, J.; Fang, A.; Yang, Y.; Qing, L.; Bi, C.; et al. Survival factor1 contributes to the oxidative stress response and is required for full virulence of Sclerotinia sclerotiorum. Mol.Plant Pathol. 2019, 20, 895–906. [CrossRef]32. Harel, A.; Bercovich, S.; Yarden, O. Calcineurin is required for sclerotial development and pathogenicity ofSclerotinia sclerotiorum in an oxalic acid–independent manner. Mol. Plant Microbe Interact. 2006, 19, 682–693.[CrossRef] [PubMed]33. Lyu, X.; Shen, C.; Fu, Y.; Xie, J.; Jiang, D.; Li, G. The microbial opsin homolog sop1 is involved in Sclerotiniasclerotiorum development and environmental stress response. Front. Microbiol. 2016, 6, 1–14. [CrossRef][PubMed]34. Liu, L.; Wang, Q.; Sun, Y.; Zhang, Y.; Zhang, X.; Liu, J. Sssfh1, a gene encoding a putative component of theRSC chromatin remodeling complex, is involved in hyphal growth, reactive oxygen species accumulation,and pathogenicity in Sclerotinia sclerotiorum. Front. Microbiol. 2018, 9, 1–14. [CrossRef] [PubMed]35. Duan, Y.; Ge, C.; Liu, S.; Wang, J.; Zhou, M. A two-component histidine kinase shk1 controls stress response,sclerotial formation and fungicide resistance in Sclerotinia sclerotiorum. Mol. Plant Pathol. 2013, 14, 708–718.[CrossRef]36. Xu, L.; Chen, W. Random T-DNA mutagenesis identifies a Cu/Zn superoxide dismutase gene as a virulencefactor of Sclerotinia sclerotiorum. Mol. Plant Microbe Interact. 2013, 26, 431–441. [CrossRef]37. Veluchamy, S.; Williams, B.; Kim, K.; Dickman, M.B. Physiological and molecular plant pathology the CuZnsuperoxide dismutase from Sclerotinia sclerotiorum is involved with oxidative stress tolerance, virulence, andoxalate production. Physiol. Mol. Plant Pathol. 2012, 78, 14–23. [CrossRef]38. Liang, Y.; Yajima, W.; Davis, M.R.; Kav, N.N.V.; Stephen, E. Disruption of a gene encoding a hypotheticalsecreted protein from Sclerotinia sclerotiorum reduces its virulence on canola (Brassica Napus) disruption of agene encoding a hypothetical secreted protein from Sclerotinia sclerotiorum reduces its virulence on Canola(Brassica napus). Can. J. Plant Pathol. 2013, 35, 46–55.39. Liang, Y.U.E.; Xiong, W.E.I.; Steinkellner, S.; Feng, J.I.E. Deficiency of the melanin biosynthesis genesSCD1 and THR1 affects sclerotial development and vegetative growth, but not pathogenicity, in Sclerotiniasclerotiorum. Mol. Plant Pathol. 2017, 19, 1–10. [CrossRef]40. Li, J.T.; Zhang, Y.H.; Zhang, Y.C.; Yu, P.L.; Pan, H.Y.; Rollins, J.A. Introduction of large sequence insertsby CRISPR-Cas9 to create pathogenicity mutants in the multinucleate filamentous pathogen Sclerotiniasclerotiorum. MBio 2018, 9, e00567-18. [CrossRef]41. Liberti, D.; Rollins, J.A.; Dobinson, K.F. Peroxysomal carnitine acetyl transferase influences host colonizationcapacity in Sclerotinia sclerotiorum. Mol. Plant Microbe Interact. 2013, 26, 768–780. [CrossRef]42. Yajima, W.; Liang, Y.; Kav, N.N.V.; Sclerotinia, A.; Bary, D. Gene disruption of an arabinofuranosidase/β-xylosidase precursor decreases Sclerotinia sclerotiorum virulence on canola tissue. Mol. Plant Microbe Interact.2009, 22, 783–789. [CrossRef] [PubMed]Pathogens 2020, 9, 27 21 of 2243. Xiao, X.; Xie, J.; Cheng, J.; Li, G.; Yi, X.; Jiang, D.; Fu, Y. Novel secretory protein Ss-Caf1 of the plant-pathogenicfungus Sclerotinia sclerotiorum is required for host penetration and normal sclerotial development. Mol. PlantMicrobe Interact. 2014, 27, 40–55. [CrossRef] [PubMed]44. Yarden, O.; Veluchamy, S.; Dickman, M.B.; Kabbage, M. Physiological and molecular plant pathologySclerotinia sclerotiorum catalase SCAT1 affects oxidative stress tolerance, regulates ergosterol levels andcontrols pathogenic development. Physiol. Mol. Plant Pathol. 2014, 85, 34–41. [CrossRef]45. Lyu, X.; Shen, C.; Fu, Y.; Xie, J.; Jiang, D.; Li, G.; Cheng, J. Comparative genomic and transcriptional analysesof the carbohydrate-active enzymes and secretomes of phytopathogenic fungi reveal their significant rolesduring infection and development. Sci. Rep. 2015, 5, 15565. [CrossRef] [PubMed]46. Yu, Y.; Jiang, D.; Xie, J.; Cheng, J.; Li, G.; Yi, X.; Fu, Y. Ss-Sl2, a novel cell wall protein with PAN modules, is essentialfor sclerotial development and cellular integrity of Sclerotinia sclerotiorum. PLoS ONE 2012, 7, e34962. [CrossRef]47. Zhang, J.; Wang, Y.; Du, J.; Huang, Z.; Fang, A.; Yang, Y. Sclerotinia sclerotiorum thioredoxin reductase isrequired for oxidative stress tolerance, virulence, and sclerotial development. Front. Microbiol. 2019, 10, 1–9.[CrossRef]48. Yu, Y.; Xiao, J.; Yang, Y.; Bi, C.; Qing, L.; Tan, W. Physiological and molecular plant pathology Ss-Bi1 encodesa putative BAX Inhibitor-1 protein that is required for full virulence of Sclerotinia sclerotiorum. Physiol. Mol.Plant Pathol. 2015, 90, 115–122. [CrossRef]49. Wang, L.; Liu, Y.; Liu, J.; Zhang, Y.; Zhang, X.; Pan, H. The Sclerotinia sclerotiorum FoxE2 gene is required forapothecial development. Mycology 2016, 106, 484–490. [CrossRef]50. Kim, H.; Chen, C.; Kabbage, M.; Dickman, M.B. Identification and characterization of Sclerotinia sclerotiorumNADPH oxidases. Appl. Environ. Microbiol. 2011, 77, 7721–7729. [CrossRef]51. Yu, Y.; Xiao, J.; Zhu, W.; Yang, Y.; Mei, J.; Bi, C.; Qian, W.E.I.; Qing, L.; Tan, W. Ss-Rhs1, a secretory Rhsrepeat-containing protein, is required for the virulence of Sclerotinia sclerotiorum. Mol. Plant Pathol. 2017, 18,1052–1061. [CrossRef]52. Fan, H.; Yu, G.; Liu, Y.; Zhang, X.; Liu, J.; Zhang, Y.; Rollins, J.A.; Sun, F.; Pan, H. An atypicalforkhead-containing transcription factor SsFKH1 is involved in sclerotial formation and is essential forpathogenicity in Sclerotinia sclerotiorum. Mol. Plant Pathol. 2017, 18, 963–975. [CrossRef] [PubMed]53. Rollins, J.A.; Pathology, P.; Hall, F. The Sclerotinia sclerotiorum pac1 gene is required for sclerotial developmentand virulence. Mol. Plant Microbe Interact. 2003, 16, 785–795. [CrossRef] [PubMed]54. Pan, Y.; Xu, Y.; Li, X.; Yao, C.; Gao, Z. Physiological and molecular plant pathology SsPemG1 encodes anelicitor-homologous protein and regulates pathogenicity in Sclerotinia sclerotiorum. Physiol. Mol. Plant Pathol.2015, 92, 70–78. [CrossRef]55. Liu, L.; Wang, Q.; Zhang, X.; Liu, J.; Zhang, Y. Ssams2, a gene encoding GATA transcription factor, is requiredfor appressoria formation and chromosome segregation in Sclerotinia sclerotiorum. Front. Microbiol. 2018, 9,1–12. [CrossRef] [PubMed]56. Jurick, W.M.; Dickman, M.B.; Rollins, J.A. Characterization and functional analysis of a CAMP-dependentprotein kinase a catalytic subunit gene (Pka1) in Sclerotinia sclerotiorum. Physiol. Mol. Plant Pathol. 2004, 64,155–163. [CrossRef]57. Chen, J.; Ullah, C.; Reichelt, M.; Gershenzon, J.; Hammerbacher, A. Sclerotinia sclerotiorum circumventsflavonoid defenses by catabolizing flavonol glycosides and aglycones. Plant Physiol. 2019, 180, 1975–1987.[CrossRef]58. Veluchamy, S.; Rollins, J.A. A CRY-DASH-type photolyase/cryptochrome from Sclerotinia sclerotiorummediatesminor UV-A-specific effects on development. Fungal Genet. Biol. 2008, 45, 1265–1276. [CrossRef]59. Li, X.L.; Guo, M.; Xu, D.F.; Chen, F.X.; Zhang, H.J.; Pan, Y.; Li, M.M.; Gao, Z. The nascent-polypeptide-associated complex alpha subunit regulates the polygalacturonases expression negatively and influences thepathogenicity of Sclerotinia sclerotiorum. Mycologia 2015, 107, 1130–1137. [CrossRef]60. Bashi, Z.D.; Gyawali, S.; Bekkaoui, D.; Coutu, C.; Lee, L.; Poon, J.; Rimmer, S.R.; Khachatourians, G.G.;Hegedus, D.D. The Sclerotinia sclerotiorum Slt2 mitogen-activated protein kinase ortholog, SMK3, is requiredfor infection initiation but not lesion expansion. Can. J. Microbiol. 2016, 850, 836–850. [CrossRef]61. Qu, X.; Yu, B.; Liu, J.; Zhang, X.; Li, G.; Zhang, D. MADS-Box transcription factor SsMADS is involved inregulating growth and virulence in Sclerotinia sclerotiorum. Int. J. Mol. Sci. 2014, 15, 8049–8062. [CrossRef]62. Zhu, W.; Wei, W.; Fu, Y.; Cheng, J.; Xie, J.; Li, G.; Yi, X. A secretory protein of necrotrophic fungus Sclerotiniasclerotiorum that suppresses host resistance. PLoS ONE 2013, 8, e53901. [CrossRef] [PubMed]Pathogens 2020, 9, 27 22 of 2263. Li, M.; Liang, X.; Rollins, J.A. Sclerotinia sclerotiorum-glutamyl transpeptidase (Ss-Ggt1) is required forregulating glutathione accumulation and development of sclerotia and compound appressoria. Mol. PlantMicrobe Interact. 2012, 25, 412–420. [CrossRef] [PubMed]64. Liang, X.; Moomaw, E.W.; Rollins, J.A. Fungal oxalate decarboxylase activity contributes to Sclerotiniasclerotiorum early infection by affecting both compound appressoria development and function.Mol. Plant Pathol. 2015, 16, 825–836. [CrossRef] [PubMed]65. Xu, L.; Xiang, M.; White, D.; Chen, W. pH dependency of sclerotial development and pathogenicity revealedby using genetically defined oxalate-minus mutants of Sclerotinia sclerotiorum. Environ. Microbiol. 2015, 17,2896–2909. [CrossRef]66. Liang, X.; Liberti, D.; Li, M.; Kim, Y.; Hutchens, A.; Wilson, R.O.N.; Rollins, J.A. Oxaloacetate acetylhydrolasegene mutants of Sclerotinia sclerotiorum do not accumulate oxalic acid, but do produce limited lesions on hostplants. Mol. Plant Pathol. 2015, 16, 559–571. [CrossRef]67. Erental, A.; Harel, A.; Yarden, O. Type 2A phosphoprotein phosphatase is required for asexual developmentand pathogenesis of Sclerotinia sclerotiorum. Mol. Plant Microbe Interact. 2007, 20, 944–954. [CrossRef]68. Li, M.; Rollins, J.A. The development-specific Ssp1 and Ssp2 genes of Sclerotinia sclerotiorum encode lectinswith distinct yet compensatory regulation. Fungal Genet. Biol. 2010, 47, 531–538. [CrossRef]69. Yu, Y.; Xiao, J.; Du, J.; Yang, Y.; Bi, C.; Qing, L. Disruption of the gene encoding endo-β-1, 4-xylanase affectsthe growth and virulence of Sclerotinia sclerotiorum. Front. Microbiol. 2016, 7, 1–9. [CrossRef]70. Ii, W.M.J.; Rollins, J.V.A. Deletion of the adenylate cyclase (Sac1) geneaffects multiple developmentalpathways and pathogenicity in Sclerotinia sclerotiorum. Fungal Genet. Biol. 2007, 44, 521–530.71. Chen, C.; Harel, A.; Gorovoits, R.; Yarden, O.; Dickman, M.B. MAPK regulation of sclerotial development inSclerotinia sclerotiorum is linked with pH and CAMP sensing. Mol. Plant Microbe Interact. 2004, 17, 404–413.[CrossRef]72. Yang, G.; Tang, L.; Gong, Y.; Xie, J.; Fu, Y.; Jiang, D.; Li, G.; Collinge, D.B.; Chen, W.; Cheng, J. A cerato-plataninprotein SsCP1 targets plant PR1 and contributes to virulence of Sclerotinia sclerotiorum. New Phytol. 2018, 217,739–755. [CrossRef] [PubMed]73. Pan, Y.; Wei, J.; Yao, C.; Reng, H.; Gao, Z. Plant science SsSm1, a cerato-platanin family protein, is involvedin the hyphal development and pathogenic process of Sclerotinia sclerotiorum. Plant Sci. 2018, 270, 37–46.[CrossRef] [PubMed]74. Zhu, G.L.; Yu, G.; Zhang, Y.H.; Rollins, J.A.; Li, J.; Pan, H. The formaldehyde dehydrogenase SsFdh1 isregulated by and functionally cooperates with the GATA transcription. MSystems 2019, 4, 1–19. [CrossRef][PubMed]75. Pan, H.; Rollins, J.A. The GATA-Type IVb zinc-finger transcription factor SsNsd1 regulates asexual—Sexualdevelopment and appressoria formation in Sclerotinia sclerotiorum. Mol. Plant Pathol. 2017, 9, 1679–1689.76. Godoy, G.; Steadman, J.R.; Dickman, M.B.; Dam, R. Use of mutants to demonstrate the role of oxalic acid inpathogenicity of Sclerotinia sclerotiorum on phaseolus vulgaris. Physiol. Mol. Plant Pathol. 1990, 37, 179–191.[CrossRef]© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open accessarticle distributed under the terms and conditions of the Creative Commons Attribution(CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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soilborne fungal pathogen
Sclerotinia sclerotiorum
fungal pathogenesis
sclerotial formation
apothecial development
fungal growth
The Notorious Soilborne Pathogenic Fungus Sclerotinia sclerotiorum: An Update on Genes Studied with Mutant Analysis
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