Draft Genome Sequences of the Turfgrass Pathogen
            <i>Sclerotinia homoeocarpa</i>

Green, Robert; Sang, Hyunkyu; Chang, Taehyun; Allan-Perkins, Elisha; Petit, Elsa; Jung, Geunhwa

doi:10.1128/genomea.01715-15

Cited by 15 publications

(12 citation statements)

References 14 publications

(17 reference statements)

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“…To find the genetic factor leading to overexpression of three CYP450s and two ABC transporters in the MDR strain, we first compared the upstream regions of CYP561 (1,314 bp), CYP65 (843 bp), CYP68 (645 bp), ShPDR1 (1,566 bp) and ShatrD (1,654 bp) between strains HRS10 and HRI11 using genome sequences generated by Green et al ( 22 ). The 459-bp upstream region of ShPDR1 and 1,000-bp upstream region of ShatrD from strains HRS10 and HRI11 were reported in previous publications ( 19 , 20 ).…”

Section: Resultsmentioning

confidence: 99%

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A Xenobiotic Detoxification Pathway through Transcriptional Regulation in Filamentous Fungi

Sang

Hulvey

Green

et al. 2018

mBio

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Fungi are known to utilize transcriptional regulation of genes that encode efflux transporters to detoxify xenobiotics; however, to date it is unknown how fungi transcriptionally regulate and coordinate different phases of detoxification system (phase I, modification; phase II, conjugation; and phase III, secretion). Here we present evidence of an evolutionary convergence between the fungal and mammalian lineages, whereby xenobiotic detoxification genes (phase I coding for cytochrome P450 monooxygenases [CYP450s] and phase III coding for ATP-binding cassette [ABC] efflux transporters) are transcriptionally regulated by structurally unrelated proteins. Following next-generation RNA sequencing (RNA-seq) analyses of a filamentous fungus, Sclerotinia homoeocarpa, the causal agent of dollar spot on turfgrasses, a multidrug resistant (MDR) field strain was found to overexpress phase I and III genes, coding for CYP450s and ABC transporters for xenobiotic detoxification. Furthermore, there was confirmation of a gain-of-function mutation of the fungus-specific transcription factor S. homoeocarpa XDR1 (ShXDR1), which is responsible for constitutive and induced overexpression of the phase I and III genes, resulting in resistance to multiple classes of fungicidal chemicals. This fungal pathogen detoxifies xenobiotics through coordinated transcriptional control of CYP450s, biotransforming xenobiotics with different substrate specificities and ABC transporters, excreting a broad spectrum of xenobiotics or biotransformed metabolites. A Botrytis cinerea strain harboring the mutated ShXDR1 showed increased expression of phase I (BcCYP65) and III (BcatrD) genes, resulting in resistance to fungicides. This indicates the regulatory system is conserved in filamentous fungi. This molecular genetic mechanism for xenobiotic detoxification in fungi holds potential for facilitating discovery of new antifungal drugs and further studies of convergent and divergent evolution of xenobiotic detoxification in eukaryote lineages.

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Section: Resultsmentioning

confidence: 99%

“…LNKV00000000). Predicted transcripts of the recently sequenced Sclerotinia homoeocarpa genomes ( 22 ) were used to guide transcript assembly by Cufflinks using the –g flag. Transcript abundance was estimated by fragments per kilobase of transcript per million fragments of mapped reads (FPKM).…”

Section: Methodsmentioning

confidence: 99%

A Xenobiotic Detoxification Pathway through Transcriptional Regulation in Filamentous Fungi

Sang

Hulvey

Green

et al. 2018

mBio

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“…The number of genes possessing certain Pfam domains was collected from Integrated Microbial Genomes (IMG/MER) for all published fungal pathogens (as of June 2017), and compared to the functional annotations for the newly sequenced lupin-infecting isolates. Fisher’s exact tests were used to assess statistical significance for over- or -under-representation of functional annotations between Sscl-Lang, Sscl-Lmut, Bcin-Lang, B. cinerea B05.10, S. sclerotiorum 1980 UF-70 [6] and S. homoeocarpa 04–21 [58]. Lupin-infecting isolates were also compared to average counts of relevant groupings of multiple isolates/species, including: lupin-infecting, legume-infecting and dicot-infecting (Additional file 1).…”

Section: Methodsmentioning

confidence: 99%

“…Whole-genome alignments were performed using MUMmer v3.1 (nucmer, data-filter, show-snps, show-coords). The Sscl-Lang and Sscl-Lmut assemblies were compared to those of S. sclerotiorum 1980 [14], S. borealis [59] and S. homoeocarpa [58]. The Bcin-Lang assembly was compared to B. cinerea B05.10 (reference isolate) [15], B. cinerea T4 [6] and B. cinerea BcDW1 [60].…”

Section: Methodsmentioning

confidence: 99%

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Mousavi‐Derazmahalleh

Chang

Thomas

et al. 2019

BMC Genomics

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Background Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea – both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts. Results Genomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum , which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents. Conclusions Detection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens. Electronic supplementary material The online version of this article (10.1186/s12864-019-5774-2) contains supplementary material, which is available to authorized users.

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“…These determinants were previously characterized in S. sclerotiorum (Xia et al, 2019), the closest fully sequenced and well characterized relative species to Clarireedia. LWC-10 and HRI11 (Green et al, 2016;Crouch et al, 2021), DRR09 and RB-19 (Crouch et al, 2021), H3 and H2 isolates, representative of C. jacksonii, C. monteithiana, and C. aff. paspali were used in this analysis.…”

Section: At the Genomic Levelmentioning

confidence: 99%

Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass

Bahri

Parvathaneni²,

Spratling³

et al. 2023

Front. Genet.

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Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, Clarireedia monteithiana and C. jacksonii (formerly Sclerotinia homoeocarpa) have been reported so far in the United States To study the Clarireedia genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced via Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as C. aff. paspali, a novel species in the United States Using short and long reads, C. aff. paspali H3 contained 193 contigs with 48.6 Mbp and presented the most completed assembly and annotation among Clarireedia species. Out of the 13,428 protein models from AUGUSTUS, 349 cytoplasmic effectors and 13 apoplastic effectors were identified by EffectorP. To further decipher Clarireedia pathogenicity, C. aff. paspali genomes (H2 and H3), as well as available C. jacksonii (LWC-10 and HRI11), C. monteithiana (DRR09 and RB-19) genomes were screened for fifty-four pathogenesis determinants, previously identified in S. sclerotiorum. Seventeen orthologs of pathogenicity genes have been identified in Clarireedia species involved in oxalic acid production (pac1, nox1), mitogen-activated protein kinase cascade (pka1, smk3, ste12), appressorium formation (caf1, pks13, ams2, rgb1, rhs1) and glycolytic pathway (gpd). Within these genes, 366 species-specific SNPs were recorded between Clarireedia species; twenty-eight were non-synonymous and non-conservative. The predicted protein structure of six of these genes showed superimposition of the models among Clarireedia spp. The genomic variations revealed here could potentially lead to differences in pathogenesis and other physiological functions among Clarireedia species.

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Draft Genome Sequences of the Turfgrass Pathogen Sclerotinia homoeocarpa

Cited by 15 publications

References 14 publications

A Xenobiotic Detoxification Pathway through Transcriptional Regulation in Filamentous Fungi

A Xenobiotic Detoxification Pathway through Transcriptional Regulation in Filamentous Fungi

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass

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