scholarly journals Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis

2020 ◽  
Vol 12 (12) ◽  
pp. 2491-2507
Author(s):  
Claudio A Valero-Jiménez ◽  
Maikel B F Steentjes ◽  
Jason C Slot ◽  
Xiaoqian Shi-Kunne ◽  
Olga E Scholten ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Gene Clusters ◽  
Single Species ◽  
White Rot ◽  
White Rot Fungus ◽  
Broad Host Range ◽  
Allium Species ◽  
Sclerotium Cepivorum ◽  
Single Host ◽  
Long Read

Abstract Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8–39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

scholarly journals Seedling infection assay for resistance to Sclerotium cepivorum in Allium species

2002 ◽  
Vol 55 ◽  
pp. 193-196 ◽  
Author(s):  
S.A. Hunger ◽  
K.L. McLean ◽  
C.C. Eady ◽  
A. Stewart
Keyword(s):  
Cultural Practices ◽  
Management Strategies ◽  
Rapid Assessment ◽  
White Rot ◽  
Allium Species ◽  
Assessment Technique ◽  
Susceptibility To Infection ◽  
Sclerotium Cepivorum ◽  
Tissue Resistance ◽  
Seedling Infection

Allium white rot (AWR) caused by the soilborne fungus Sclerotium cepivorum is the most devastating disease in onion crops worldwide Integrated pest management strategies involving cultural practices biocontrol agents genetic engineering and selective breeding are being investigated to control this disease A major obstacle to evaluating these different methods is the lack of a simple accurate rapid assessment technique for AWR pathogenesis An assay for quantifying AWR tissue resistance in Allium species has been developed Lesion development on Allium seedlings was used as an indicator of susceptibility to infection A difference in AWR resistance between leek and onion seedlings was detected using this assessment technique with infection scores of 13 and 5456 respectively Leek seedlings exhibited less frequent and less extensive lesions than the onion seedlings Engineered germplasm onion cultivars and other related Allium species with varying degrees of susceptibility to AWR will be screened using this assay to calibrate levels of AWR resistance

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum . In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

Effect of Neem Oil (Azadirachtin) Against White Rot Fungus (Polyporous Versicolor) in Wood Plastic Particle Board

2012 ◽  
Vol 3 (1) ◽  
pp. 20-21
Author(s):  
A.Sangeetha A.Sangeetha ◽  
◽  
K.Thanigai K.Thanigai ◽  
Narasimhamurthy Narasimhamurthy ◽  
S.K.Nath S.K.Nath
Keyword(s):  
White Rot ◽  
White Rot Fungus ◽  
Particle Board ◽  
Neem Oil ◽  
Plastic Particle

Effects of White Rot Fungus Physisporinus sp., Isolated in Japan, on Styrene-butadiene Rubber

2020 ◽  
Vol 93 (9) ◽  
pp. 289-292
Author(s):  
Yumi SHIMIZU ◽  
Shuma SATHO ◽  
Taro NAKAJIMA ◽  
Hiroaki KOUZAI ◽  
Kiminori SHIMIZU
Keyword(s):  
White Rot ◽  
White Rot Fungus ◽  
Styrene Butadiene Rubber ◽  
Butadiene Rubber ◽  
Styrene Butadiene

Genome sequence of Novosphingobium malaysiense strain MUSC 273T, novel alpha-proteobacterium isolated from intertidal soil

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
Nurul-Syakima Ab Mutalib ◽  
Learn-Han Lee
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Genome Sequence ◽  
Catalase Activity ◽  
Gene Clusters ◽  
Rrna Genes ◽  
Gram Negative ◽  
Genomic Features

Novosphingobium malaysiense strain MUSC 273T is a recently identified Gram-negative, aerobic alpha-proteobacterium. The strain was isolated from intertidal soil with strong catalase activity. The genome sequence comprises 5,027,021 bp, with 50 tRNA and 3 rRNA genes. Further analysis identified presence of secondary metabolite gene clusters within genome of MUSC 273T. Knowledge of the genomic features of the strain may allow further biotechnological exploitation, particularly for production of secondary metabolites as well as production of industrially important enzymes

Synergistic Methodology Based on Ion Exchange and Biodegradation Mechanisms Applied for Metal Complex Dye Removal from Waste Waters

2018 ◽  
Vol 69 (1) ◽  
pp. 38-44
Author(s):  
Nicoleta Mirela Marin ◽  
Olga Tiron ◽  
Luoana Florentina Pascu ◽  
Mihaela Costache ◽  
Mihai Nita Lazar ◽  
...  
Keyword(s):  
Ion Exchange ◽  
Synergistic Effects ◽  
Freundlich Isotherm ◽  
White Rot ◽  
White Rot Fungus ◽  
Basic Anion Exchange Resin ◽  
Km Value ◽  
Points Of View ◽  
Basic Anion

This study investigates the synergistic effects of ion exchange and biodegradation methods to remove the Acid Blue 193 also called Gryfalan Navy Blue RL (GNB) dye from wastewater. Ion exchange studies were performed using a strongly basic anion exchange resin Amberlite IRA 400. The equilibrium was characterized by a kinetic and thermodynamic points of view, establishing that the sorption of the GNB dye was subject to the Freundlich isotherm model with R2 = 0.8710. Experimental results showed that the activated resin can removed up to 93.4% when the concentration of dye solution is 5.62�10-2 mM. The biodegradation of the GNB was induced by laccase, an enzyme isolated from white-rot fungus. It was also analyzed the role of pH and dye concentration on GNB biodegradation, so 5�10-2 mM dye had a maximum discoloration efficiency of 82.9% at pH of 4. The laccase showed a very fast and robust activity reaching in a few minutes a Km value of 2.2�10-1mM. In addition, increasing the GNB concentration up to 8�10-1 mM did not triggered a substrat inhibition effect on the laccase activity. Overall, in this study we proposed a mixt physicochemical and biological approach to enhance the GNB removal and biodegradability from the wastewaters and subsequently the environment.

Sign in / Sign up

Export Citation Format

Share Document