scholarly journals First Draft Genome Sequence Resource of a Strain of Pseudocercospora fijiensis Isolated in North America

2020 ◽  
Vol 110 (10) ◽  
pp. 1620-1622
Author(s):  
Luis Amarillas ◽  
Mitzi Estrada-Acosta ◽  
Rubén G. León-Chan ◽  
Carlos López-Orona ◽  
Luis Lightbourn
Keyword(s):  
North America ◽  
Fungicide Resistance ◽  
Fungal Pathogens ◽  
Genomic Sequence ◽  
Draft Genome ◽  
Bioinformatic Analysis ◽  
Black Sigatoka ◽  
Efficient Management ◽  
Black Sigatoka Disease ◽  
Pseudocercospora Fijiensis

Black Sigatoka disease, caused by the fungus Pseudocercospora fijiensis, is one of the most devastating diseases of banana around the world. Fungicide applications are the primary tool used to manage black Sigatoka, but fungicide resistance in P. fijiensis, as in other fungal pathogens, is one of the major limitations in the efficient management and prevention of this disease. In the current study, we present the draft genome of P. fijiensis strain IIL-20, the first genomic sequence published from a strain of this fungus isolated in North America. Bioinformatic analysis showed putative genes involved in fungus virulence and fungicide resistance. These findings may lead us to a better understanding of the molecular pathogenesis of this fungal pathogen and also to the discovery of the mechanisms conferring fungicide resistance.

scholarly journals Inelastic scattering imaging system for Pseudocercospora fijiensis detection

2019 ◽  
Author(s):  
Juan Velez Alvarez ◽  
Alvaro Bastidas ◽  
Alejandra Monsalve ◽  
Tehseen Adel ◽  
Isabel Calle ◽  
...  
Keyword(s):  
Inelastic Scattering ◽  
Imaging System ◽  
Culture Media ◽  
Black Sigatoka ◽  
Bending Vibration ◽  
Fungal Cell ◽  
Industrial Economy ◽  
Fungal Phytopathogen ◽  
Black Sigatoka Disease ◽  
Pseudocercospora Fijiensis

This work sought to develop an inelastic scattering imaging system based on Raman spectroscopy for the detection of the fungal phytopathogen, Pseudocercospora fijiensis, which causes Black Sigatoka disease in banana crops, very important in Colombian agro-industrial economy. This system consists of a modified stereoscope with an optical setup able to simultaneously capture spectral images together with its Raman spectra. The camera has two different bandpass filters attached, centered in the spectral region of C=O stretching of Chitin and the equatorial bending vibration of beta-1,3-glucan, molecules of the fungal cell wall. In this way, the system can get images with unique spectral features, suitable for training a convolutional neural network in order to get a recognition pattern of the fungal strain growing in the PDA agar. As a result, the instrument was able to detect the presence of P.fijiensis over the culture media.

scholarly journals Inelastic scattering imaging system for Pseudocercospora fijiensis detection

2019 ◽  
Author(s):  
Juan Velez Alvarez ◽  
Alvaro Bastidas ◽  
Alejandra Monsalve ◽  
Tehseen Adel ◽  
Isabel Calle ◽  
...  
Keyword(s):  
Inelastic Scattering ◽  
Imaging System ◽  
Culture Media ◽  
Black Sigatoka ◽  
Bending Vibration ◽  
Fungal Cell ◽  
Industrial Economy ◽  
Fungal Phytopathogen ◽  
Black Sigatoka Disease ◽  
Pseudocercospora Fijiensis

This work sought to develop an inelastic scattering imaging system based on Raman spectroscopy for the detection of the fungal phytopathogen, Pseudocercospora fijiensis, which causes Black Sigatoka disease in banana crops, very important in Colombian agro-industrial economy. This system consists of a modified stereoscope with an optical setup able to simultaneously capture spectral images together with its Raman spectra. The camera has two different bandpass filters attached, centered in the spectral region of C=O stretching of Chitin and the equatorial bending vibration of beta-1,3-glucan, molecules of the fungal cell wall. In this way, the system can get images with unique spectral features, suitable for training a convolutional neural network in order to get a recognition pattern of the fungal strain growing in the PDA agar. As a result, the instrument was able to detect the presence of P.fijiensis over the culture media.

scholarly journals Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism

Pathogens ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 232 ◽  
Author(s):  
Rong Xu ◽  
Xiaochen Liu ◽  
Bing Peng ◽  
Peibin Liu ◽  
Zhuang Li ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
De Novo ◽  
Genomic Sequence ◽  
Management Strategies ◽  
Gene Families ◽  
Morphological Characterization ◽  
Edible Mushrooms ◽  
Efficient Management ◽  
Pathogenic Genes ◽  
Cobweb Disease

Cladobotryum dendroides, which causes cobweb disease in edible mushrooms, is one of the major fungal pathogens. Our previous studies focused on the genetic and morphological characterization of this fungus, as well as its pathogenicity and the identification of appropriate fungicides. However, little is known about the genome characters, pathogenic genes, and molecular pathogenic mechanisms of C. dendroides. Herein, we reported a high-quality de novo genomic sequence of C. dendroides and compared it with closely-related fungi. The assembled C. dendroides genome was 36.69 Mb, consisting of eight contigs, with an N50 of 4.76 Mb. This genome was similar in size to that of C. protrusum, and shared highly conserved syntenic blocks and a few inversions with C. protrusum. Phylogenetic analysis revealed that, within the Hypocreaceae, Cladobotryum was closer to Mycogone than to Trichoderma, which is consistent with phenotypic evidence. A significant number of the predicted expanded gene families were strongly associated with pathogenicity, virulence, and adaptation. Our findings will be instrumental for the understanding of fungi–fungi interactions, and for exploring efficient management strategies to control cobweb disease.

scholarly journals Draft Genome Sequence of Streptomyces sp. TP-A0874, a Catechoserine Producer

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Hisayuki Komaki ◽  
Akira Hosoyama ◽  
Natsuko Ichikawa ◽  
Yasuhiro Igarashi
Keyword(s):  
Genome Sequence ◽  
Cell Invasion ◽  
Draft Genome ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
Tumor Cell Invasion ◽  
Draft Genome Sequence ◽  
Biosynthetic Gene ◽  
Streptomyces Sp

We report the draft genome sequence of Streptomyces sp. TP-A0874 isolated from compost. This strain produces catechoserine, a new catecholate-type inhibitor of tumor cell invasion. The genome harbors at least six gene clusters for polyketide and nonribosomal peptide biosyntheses. The biosynthetic gene cluster for catechoserines was identified by bioinformatic analysis.

scholarly journals The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

2010 ◽  
Vol 9 (1) ◽  
pp. 55-69 ◽  
Author(s):  
Christopher D. Shaffer ◽  
Consuelo Alvarez ◽  
Cheryl Bailey ◽  
Daron Barnard ◽  
Satish Bhalla ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Undergraduate Research ◽  
Bioinformatic Analysis ◽  
Ongoing Research ◽  
The Core ◽  
Undergraduate Institutions ◽  
Genomics Research ◽  
Genomics Education ◽  
Washington University ◽  
Genome Center

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

scholarly journals Succinate dehydrogenase inhibitor (SDHI) fungicide resistance prevention strategy

2011 ◽  
Vol 64 ◽  
pp. 119-124 ◽  
Author(s):  
A.H. McKay ◽  
G.C. Hagerty ◽  
G.B. Follas ◽  
M.S. Moore ◽  
M.S. Christie ◽  
...  
Keyword(s):  
New Zealand ◽  
High Risk ◽  
Succinate Dehydrogenase ◽  
Fungicide Resistance ◽  
Fungal Pathogens ◽  
Resistance Management ◽  
Resistance Development ◽  
Development Of Resistance ◽  
Action Committee ◽  
Succinate Dehydrogenase Inhibitor

Succinate dehydrogenase inhibitor (SDHI) fungicides are currently represented in New Zealand by eight active ingredients bixafen boscalid carboxin fluaxapyroxad fluopyram isopyrazam penthiopyrad and sedaxane They are either currently registered or undergoing development in New Zealand for use against a range of ascomycete and basiodiomycete pathogens in crops including cereals ryegrass seed apples pears grapes stonefruit cucurbits and kiwifruit These fungicides are considered to have medium to high risk of resistance development and resistance management is recommended by the Fungicide Resistance Action Committee (FRAC) in Europe Guidelines are presented for use of SDHI fungicides in New Zealand to help avoid or delay the development of resistance in the fungal pathogens that they target

scholarly journals An analysis of postharvest fungal pathogens reveals temporal-spatial and host-pathogen associations with fungicide resistance-related mutations

2021 ◽  
Author(s):  
Michael Bradshaw ◽  
Holly Packard Bartholomew ◽  
Dylan Hendricks ◽  
Autumn Maust ◽  
Wayne Jurick II
Keyword(s):  
Fungicide Resistance ◽  
Fungal Pathogens ◽  
Meta Analysis ◽  
Management Strategies ◽  
Amino Acid Position ◽  
Plant Host ◽  
Wide Range ◽  
Total Data ◽  
Fungal Phytopathogens ◽  
Β Tubulin

Fungicides are the primary tools to control a wide range of postharvest fungal pathogens. Fungicide resistance is a widespread problem that has reduced fungicide efficacy. Resistance to FRAC 1 chemistries are associated with mutations in amino acid position 198 in the β-tubulin gene. In the current study we conducted a meta-analysis of β-tubulin sequences to infer temporal, spatial, plant host and pathogen genus patterns of fungicide resistance in postharvest fungal pathogens. In total, data was acquired from 2647 specimens from 12 genera of fungal phytopathogens residing in 53 countries, on over 200 hosts collected between 1926-2020. The specimens containing a position 198 mutation were globally distributed in a variety of pathosystems. Analyses showed that there is an association between the mutation and the year an isolate was collected, the pathogen genus, the pathogen host and the collection region. Interestingly, fungicide resistant β-tubulin genotypes have been in a decline since their peak between 2005-2009. FRAC 1 fungicide usage data followed a similar pattern in that applications have been in a decline since their peak between 1997 and 2003. The data shows that, with the reduction of selection pressure, FRAC 1 fungicide resistance in fungal populations will decline within 5-10 years. Based on this line of evidence, we contend that a β-tubulin position 198 mutation has uncharacterized fitness cost(s) on fungi in nature. The compiled dataset can inform end users on the regions and hosts that are most prone to contain resistant pathogens and assist decisions concerning fungicide resistant management strategies.

scholarly journals A time series forecasting of the proportion of SARS-CoV-2 N501Y lineage in North America

2021 ◽  
Author(s):  
Elena Quinonez ◽  
Majid Vahed ◽  
Abdolrazagh Hashemi Shahraki ◽  
Mehdi Mirsaeidi
Keyword(s):  
Time Series ◽  
North America ◽  
South African ◽  
Neutralizing Antibodies ◽  
Genomic Sequence ◽  
Natural Infection ◽  
Rapid Evolution ◽  
Neutralizing Antibody ◽  
Time Series Forecasting ◽  
Global Database

Introduction: The outbreak of pneumonia known as SARS-COV-2 and newly-emerging South African (B.1.351), the United Kingdom (B.1.1.7) and Brazil (P.1) variants have led to a more infectious virus and potentially more substantial loss of neutralizing activity by natural infection or vaccine-elicited antibodies. Methods: We identified prevalent mutations using the spike receptor-binding domain (S-RBD) of SARS-CoV-2 deposited in the Nextstrain global database and comparing them to the Wuhan-Hu-1/2019 genomic sequence as a reference. Then we calculated the percentages of mutant genomes from the total regional subsample isolates from December 2019 to the end of January 2021. We developed two separate time series forecasting models for the SARS-CoV-2 B.1.1.7 variant. The computational model used the structure of the S-RBD to examine its interactions with the neutralizing antibody, named CV30 (isolated from a patient), and human angiotensin-converting enzyme 2 (hACE-2), based on a hybrid algorithm of template-based modeling to predict the affinity of S protein to the neutralizing antibodies and hACE-2 receptor. Results: The proportion of the B.1.1.7 strain in North America is growing fast. From these computations, it seems that the S-RBD and hACE-2 proteins are less favorable for the South African strain (K417N, E484K, and N501Y) as compared to the wild type structure and more favorable for B.1.1.7 and P.1 variants. In the present of crystallized CV30 neutralizing antibodies, docking scores suggest antibodies can be partially neutralize the B.1.1.7 variant, and, less efficiently, the B.1.351 and P.1 variants. Conclusion: The rapid evolution of SARS-CoV-2 has the potential to allow the newly-emerged B.1.351, and P.1 variants to escape from natural or vaccine-induced neutralizing immunity and viral spreading.

scholarly journals Can High-Risk Fungicides be Used in Mixtures Without Selecting for Fungicide Resistance?

2014 ◽  
Vol 104 (4) ◽  
pp. 324-331 ◽  
Author(s):  
Alexey Mikaberidze ◽  
Bruce A. McDonald ◽  
Sebastian Bonhoeffer
Keyword(s):  
High Risk ◽  
Disease Control ◽  
Fungicide Resistance ◽  
Fungal Pathogens ◽  
Development Of Resistance ◽  
Population Dynamics Model ◽  
Fungicide Mixtures ◽  
Cost Of Resistance ◽  
Selection For ◽  
Crucial Parameter

Fungicide mixtures produced by the agrochemical industry often contain low-risk fungicides, to which fungal pathogens are fully sensitive, together with high-risk fungicides known to be prone to fungicide resistance. Can these mixtures provide adequate disease control while minimizing the risk for the development of resistance? We present a population dynamics model to address this question. We found that the fitness cost of resistance is a crucial parameter to determine the outcome of competition between the sensitive and resistant pathogen strains and to assess the usefulness of a mixture. If fitness costs are absent, then the use of the high-risk fungicide in a mixture selects for resistance and the fungicide eventually becomes nonfunctional. If there is a cost of resistance, then an optimal ratio of fungicides in the mixture can be found, at which selection for resistance is expected to vanish and the level of disease control can be optimized.

Sign in / Sign up

Export Citation Format

Share Document