4.4 Article

Deep amplicon sequencing reveals extensive allelic diversity in the erg11/ CYP51 promoter and allows multi-population DMI fungicide resistance monitoring in the canola pathogen Leptosphaeria maculans

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

The population genetics of adaptation through copy number variation in a fungal plant pathogen

Luzia Stalder et al.

Summary: This study analyzes how a fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. The research shows that gene duplications and deletions are major sources of adaptive genetic variation, with most gene duplications resulting from segmental chromosomal duplications. The pathogen utilizes these adaptive genetic variations to exploit the host and resist fungicides.

MOLECULAR ECOLOGY (2023)

Article Plant Sciences

Optimized Sample Processing Pipeline for PCR-Based Fungicide Resistance Quantification of Stubble-Borne Fungal Pathogens

Leon M. Hodgson et al.

Summary: Globally, the increasing problem of yield losses due to failed crop protection caused by fungicide-resistant pathogens is being addressed. A study was conducted to assess the fungicide resistance of the barley pathogen Pyrenophora teres f. teres in stubble samples. Different methods were employed to extract and purify fungal DNA, and the chip-digital PCR assay was used to quantify fungicide resistance. The study developed molecular pipeline options for pathogen fungicide resistance quantification from cereal stubbles, providing guidance for improved crop protection outcomes.

PHYTOPATHOLOGY (2023)

Article Agronomy

Emergence of Fungicide Sensitivity in Leptosphaeria maculans Isolates Collected from the Czech Republic to DMI Fungicides

Olufadekemi Fajemisin et al.

Summary: This study aimed to investigate the sensitivity of Leptosphaeria maculans isolates collected in the Czech Republic to three fungicides and found the potential presence of resistant isolates.

AGRICULTURE-BASEL (2022)

Article Genetics & Heredity

Multiple scenarios for sexual crosses in the fungal pathogen Zymoseptoria tritici on wheat residues: Potential consequences for virulence gene transmission

Carolina Orellana-Torrejon et al.

Summary: This study demonstrates that sexual reproduction in Zymoseptoria tritici does not necessarily require symptomatic infection in plant tissues, as avirulent strains can reproduce sexually without causing plant symptoms. Furthermore, the intensity of asexual and sexual reproduction does not differ significantly between different co-inoculation scenarios, suggesting that crosses involving avirulent strains are not rare events.

FUNGAL GENETICS AND BIOLOGY (2022)

Article Agronomy

Azole fungicide sensitivity and molecular mechanisms of reduced sensitivity in Irish Pyrenopeziza brassicae populations

Diana E. Bucur et al.

Summary: This study investigated the sensitivity of Irish populations of Pyrenopeziza brassicae, the causal agent of light leaf spot, to azole fungicides and genotyped the PbCYP51 gene. The results showed a variation in sensitivity to azole fungicides among Irish isolates, with differences in sensitivity to tebuconazole. Two substitutions and varying sizes of inserts were found in PbCYP51, and the presence of the G460S/S508T double mutant was reported for the first time. The study suggests that azole fungicides are still effective in controlling light leaf spot in Ireland, but recommends their use in mixture with fungicides having different modes of action.

PEST MANAGEMENT SCIENCE (2022)

Article Genetics & Heredity

Analysis of Cyp51 protein sequences shows 4 major Cyp51 gene family groups across fungi

Brandi N. Celia-Sanchez et al.

Summary: Azole drugs are commonly used to treat fungal infections, but resistance to these drugs has been observed in several fungal pathogens. In this study, the researchers focused on the resistance mechanism in Aspergillus fumigatus and found that it arises from mutations in the coding sequence and tandem repeats in the promoter region of cyp51A. They also investigated the presence of Cyp51 proteins in various fungi and found that filamentous Ascomycota have both Cyp51A and Cyp51B paralogs, while only 50% of them have the Cyp51A paralog.

G3-GENES GENOMES GENETICS (2022)

Article Biotechnology & Applied Microbiology

Strainline: full-length de novo viral haplotype reconstruction from noisy long reads

Xiao Luo et al.

Summary: Researchers have introduced a novel approach called Strainline that allows for the assembly of viral haplotypes from noisy long reads without a reference genome. Benchmarking on simulated and real datasets of varying complexity and diversity confirms the novelty and superiority of Strainline.

GENOME BIOLOGY (2022)

Article Agronomy

Mutation incyp51band overexpression ofcyp51aandcyp51bconfer multiple resistant toDMIsfungicide prochloraz inFusarium fujikuroi

Yu Zhang et al.

Summary: Prochloraz-resistant strains of Fusarium fujikuroi were found in agricultural regions of Zhejiang Province, China, with a point mutation (S312T) in the FfCYP51B protein being identified as the mechanism of resistance. Exchange of the CYP51B locus confirmed that this mutation confers resistance to prochloraz, and qRT-PCR analysis revealed up-regulation of Ffcyp51a and Ffcyp51b in resistant strains. Docking analysis indicated increased affinity between prochloraz and FfCYP51B after the S312T mutation.

PEST MANAGEMENT SCIENCE (2021)

Review Plant Sciences

Epidemiology and management of blackleg of canola in response to changing farming practices in Australia

Angela P. Van de Wouw et al.

Summary: The Australian canola industry has seen rapid growth in recent years, with growers and agronomists adopting modern management practices to increase yield, such as increasing crop residue retention and using resistant varieties and hybrids. However, some of these changes have also increased the risk and severity of diseases, highlighting the need for new strategies for disease control.

AUSTRALASIAN PLANT PATHOLOGY (2021)

Article Biochemical Research Methods

New strategies to improve minimap2 alignment accuracy

Heng Li

Summary: The latest version of minimap2 v2.22 has made improvements in accurately mapping long reads to highly repetitive regions and in allowing alignments through insertions or deletions up to 100 kb by default, addressing major weaknesses in earlier versions.

BIOINFORMATICS (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Agronomy

A world-wide analysis of reduced sensitivity to DMI fungicides in the banana pathogen Pseudocercospora fijiensis

Pablo Chong et al.

Summary: This study found a continuous range of sensitivity to sterol demethylation inhibitors in Pseudocercospora fijiensis field isolates collected from different banana production zones in various countries, with clear cross-sensitivity. Sequence analysis of PfCYP51 revealed 28 independent amino acid substitutions, nine of which correlated with reduced sensitivity to DMIs.

PEST MANAGEMENT SCIENCE (2021)

Article Agriculture, Multidisciplinary

Fungicide sensitivity and resistance in the blackleg fungus, Leptosphaeria maculans, across canola growing regions in Australia

A. P. Van de Wouw et al.

Summary: The use of fungicides is widespread in canola-growing regions of Australia to combat blackleg disease caused by Leptosphaeria maculans. While resistance to demethylation inhibitor (DMI) fungicides is common, there is also evidence of potential cross-resistance to a newer class of fungicides, highlighting the importance of proactive surveillance to maintain fungicide efficacy.

CROP & PASTURE SCIENCE (2021)

Article Computer Science, Interdisciplinary Applications

colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes

Achim Zeileis et al.

JOURNAL OF STATISTICAL SOFTWARE (2020)

Article Computer Science, Interdisciplinary Applications

Various Versatile Variances: An Object-Oriented Implementation of Clustered Covariances in R

Achim Zeileis et al.

JOURNAL OF STATISTICAL SOFTWARE (2020)

Review Microbiology

The Fungal CYP51s: Their Functions, Structures, Related Drug Resistance, and Inhibitors

Jingxiang Zhang et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Agriculture, Multidisciplinary

Changes in allele frequencies of avirulence genes in the blackleg fungus, Leptosphaeria maculans, over two decades in Australia

Angela P. Van de Wouw et al.

CROP & PASTURE SCIENCE (2018)

Article Agriculture, Multidisciplinary

Changes in farming practices impact on spore release patterns of the blackleg pathogen, Leptosphaeria maculans

J. McCredden et al.

CROP & PASTURE SCIENCE (2018)

Article Biotechnology & Applied Microbiology

Variation graph toolkit improves read mapping by representing genetic variation in the reference

Erik Garrison et al.

NATURE BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Fabien Dutreux et al.

SCIENTIFIC DATA (2018)

Article Biochemistry & Molecular Biology

De novo assembly of viral quasispecies using overlap graphs

Jasmijn A. Baaijens et al.

GENOME RESEARCH (2017)

Article Multidisciplinary Sciences

BBMerge - Accurate paired shotgun read merging via overlap

Brian Bushnell et al.

PLOS ONE (2017)

Article Multidisciplinary Sciences

Azole sensitivity in Leptosphaeria pathogens of oilseed rape: the role of lanosterol 14α-demethylase

Thomas R. Sewell et al.

SCIENTIFIC REPORTS (2017)

Article Biotechnology & Applied Microbiology

Near-optimal probabilistic RNA-seq quantification

Nicolas L. Bray et al.

NATURE BIOTECHNOLOGY (2016)

Article Plant Sciences

A Global Analysis of CYP51 Diversity and Azole Sensitivity in Rhynchosporium commune

Patrick C. Brunner et al.

PHYTOPATHOLOGY (2016)

Article Agronomy

Azole fungicides-understanding resistance mechanisms in agricultural fungal pathogens

Claire L. Price et al.

PEST MANAGEMENT SCIENCE (2015)

Article Multidisciplinary Sciences

Dose-Response Analysis Using R

Christian Ritz et al.

PLOS ONE (2015)

Article Biochemical Research Methods

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

Jian Ye et al.

BMC BIOINFORMATICS (2012)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Review Agriculture, Multidisciplinary

A century of fungicide evolution

PE Russell

JOURNAL OF AGRICULTURAL SCIENCE (2005)

Article Biotechnology & Applied Microbiology

Tandem repeat of a transcriptional enhancer upstream of the sterol 14α-demethylase gene (CYP51) in Penicillium digitatum

H Hamamoto et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2000)