scholarly journals High Contiguity Whole Genome Sequence and Gene Annotation Resource for Two Venturia nashicola Isolates

2019 ◽  
Vol 32 (9) ◽  
pp. 1091-1094 ◽  
Author(s):  
Maxim Prokchorchik ◽  
Kyungho Won ◽  
Yoonyoung Lee ◽  
Eu Ddeum Choi ◽  
Cécile Segonzac ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Data ◽  
Asian Pear ◽  
Venturia Nashicola ◽  
Host Range Determination ◽  
Range Determination ◽  
Northeast Asian

Venturia nashicola is a fungal pathogen that causes Asian pear scab disease. This pathogen is of particular importance in Northeast Asian countries, where Asian pears are grown industrially. Scab disease in Asian pear is currently controlled by fungicide spraying and this situation calls for developing scab resistant cultivars. High-quality genome data are therefore required for in-depth comparative genome analysis of different isolates of V. nashicola and V. pyrina, a closely related species, which only infects European pear plants. Here, we report the high-contiguity whole genome assembly of two V. nashicola isolates, which is expected to enable genome comparisons for identification of the genes involved in host range determination of V. nashicola.

scholarly journals Whole Genome Sequence Resource of the Asian Pear Scab Pathogen Venturia nashicola

2019 ◽  
Vol 32 (11) ◽  
pp. 1463-1467 ◽  
Author(s):  
Shakira Johnson ◽  
Dan Jones ◽  
Amali H. Thrimawithana ◽  
Cecilia H. Deng ◽  
Joanna K. Bowen ◽  
...  
Keyword(s):  
Host Specificity ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Nonhost Resistance ◽  
Whole Genome ◽  
European Pear ◽  
Asian Pear ◽  
Pear Scab ◽  
Venturia Nashicola ◽  
Biotrophic Fungus

Venturia nashicola, the cause of scab disease of Asian pears, is a host-specific, biotrophic fungus. It is restricted to Asia and is regarded as a quarantine threat outside this region. European pear displays nonhost resistance (NHR) to V. nashicola and Asian pears are nonhosts of V. pyrina (the cause of European pear scab disease). The host specificity of these two fungi is likely governed by differences in their effector arsenals, with a subset hypothesized to activate NHR. The Pyrus-Venturia pathosystem provides an opportunity to dissect the underlying genetics of nonhost interactions in this potentially more durable form of resistance. The V. nashicola genome will enable comparisons to other Venturia spp. genomes to identify effectors that potentially activate NHR in the pear scab pathosystem.

scholarly journals Determination of whole-genome sequence of Salmonella Abortusequi

2016 ◽  
Vol 39 ◽  
pp. S59 ◽  
Author(s):  
H. Niwa ◽  
M. Akiba ◽  
T. Sekizuka ◽  
M. Kuroda ◽  
Y. Kinoshita ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome

scholarly journals Draft Genome Sequence of the Asian Pear Scab Pathogen, Venturia nashicola

2018 ◽  
Author(s):  
Shakira Johnson ◽  
Dan Jones ◽  
Amali H. Thrimawithana ◽  
Cecilia H. Deng ◽  
Joanna K. Bowen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Host Resistance ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Close Relative ◽  
Prevention Measures ◽  
European Pear ◽  
Asian Pear ◽  
Pear Scab ◽  
Venturia Nashicola

AbstractVenturia nashicola, which causes scab disease of Asian pear, is a host-specific, biotrophic fungus, with a sexual stage that occurs during saprobic growth. V. nashicola is endemic to Asia and is regarded as a quarantine threat to Asian pear production outside of this continent. Currently, fungicide applications are routinely used to control scab disease. However, fungicide resistance in V. nashicola, as in other fungal pathogens, is an ongoing challenge and alternative control or prevention measures that include, for example, the deployment of durable host resistance, are required. A close relative of V. nashicola, V. pirina, causes scab disease of European pear. European pear displays non-host resistance (NHR) to V. nashicola and Asian pears are non-hosts of V. pirina. It is anticipated that the host specificity of these two fungi is governed by differences in their effector arsenals, with a subset responsible for activating NHR. The Pyrus-Venturia pathosystems provide a unique opportunity to dissect the underlying genetics of non-host interactions and to understand coevolution in relation to this potentially more durable form of resistance. Here, we present the first V. nashicola draft whole genome sequence (WGS), which is made up of 40,800 scaffolds (totalling 45 Mb) and 11,094 predicted genes. Of these genes, 1,232 are predicted to encode a secreted protein by SignalP, with 273 of these predicted to be effectors by EffectorP. The V. nashicola WGS will enable comparison to the WGSs of other Venturia spp. to identify effectors that potentially activate NHR in the pear scab pathosystems.

scholarly journals Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000

2021 ◽  
Author(s):  
James Tambong ◽  
Renlin Xu ◽  
Diane Cuppels ◽  
Julie T Chapados ◽  
suzanne Gerdis ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Coding ◽  
Genome Data ◽  
Bacterial Speck Disease

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Here, we report 33 whole genome sequences of Canadian strains of P. syringae pv. tomato isolated in Ontario, Canada, between 1992 and 2008. The genome sequences exhibited average nucleotide identity values of 98.64-98.72 % with P. syringae pv. tomato ICMP 2844PT and DC3000, validating the taxonomic standing of these Canadian strains. The genome sizes ranged from 6.20-6.39 Mbp with G+C content of 58.6% and comprised 5,889-6,166 protein-coding sequences (CDSs). The strains had pan- and core-genomes of 6808 and 4,993 gene clusters, respectively. Genome mining of the strains for virulence factors identified typical adherence genes, proteins related to antiphagocytosis, secretion system apparatuses and effectors. Also, partial or complete achromobactin biosynthetic cluster and iron transport genes were identified in all the Canadian strains but absent in P. syringae pv. tomato DC3000 or ICMP 2844 (pathotype). These new whole genome data of Canadian strains of P. syringae pv. tomato could be useful resources in understanding the evolution of this pathogen.

scholarly journals Whole genome sequence and gene annotation resource for Didymella bellidis, associated with tea leaf spot

Plant Disease ◽  
2020 ◽  
Author(s):  
Xue Wang ◽  
Xian Wu ◽  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Leaf Spot ◽  
Sequence Data ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Whole Genome

Didymella bellidis is a phytopathogenic fungus that causes leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in Guizhou Province, China. D. bellidis isolate GZYQYQX2B was sequenced using Pacific Biosciences and Illumina technologies, and assembled into a whole genome of 35.5 Mbp. Transcripts of D. bellidis isolate GZYQYQX2B were predicted from the assembled genome and were further validated by RNA sequence data. In total, 10,731 genes were predicted by integrating three approaches, namely ab initio and homology-based gene prediction, as well as transcriptomics data. The whole-genome sequence of D. bellidis will provide a resource for future research on trait-specific genes of the pathogen and host-pathogen interactions.

scholarly journals Quaternary ammonium compound resistance as a persistence marker for L. monocytogenes

2020 ◽  
Author(s):  
Ashley L Cooper ◽  
Catherine D Carrillo ◽  
Mylène Deschênes ◽  
Burton Blais
Keyword(s):  
Quaternary Ammonium ◽  
Gene Cassette ◽  
Whole Genome Sequence ◽  
Ammonium Compound ◽  
Whole Genome ◽  
Food Manufacturing ◽  
Risk Managers ◽  
Manufacturing Environments ◽  
Contamination Events

Persistent contamination of food manufacturing environments by Listeria monocytogenes is an important public health risk because such contamination events defy standard sanitization protocols, for example, the application of quaternary ammonium compounds such as benzalkonium chloride (BC), providing a source for prolonged dissemination of the bacteria in food products. We performed whole-genome sequence (WGS) analyses of 1279 well-characterized L. monocytogenes isolates from a variety of foods and food manufacturing environments and identified the bcrABC gene cassette associated with BC resistance in 41.5% of isolates. Of particular interest was the finding that all but one of 177 clonal complex (CC) 321 isolates, representing one of the most commonly occurring CCs found in foods and food-production environments, harbored the intact bcrABC cassette. Thirty-nine (38.6) percent of isolates recovered from foods representing 67 different CCs, and 59.2% of strains from food-manufacturing environmental samples representing 26 different CCs, were found to harbor the intact bcrABC cassette. A representative set of 69 isolates with and without bcrABC was assayed for the ability to grow in the presence of BC, and 34 of 35 isolates harboring the bcrABC cassette were resistant to BC. Determination of bcrABC in colony isolates could be achieved using both polymerase chain reaction and whole genome sequencing techniques, providing food testing laboratories with options for the characterization of isolates. The ability to detect bcrABC provides risk managers with a valuable tool to assess the potential for persistent contamination of the food manufacturing environment, which in turn may indicate the need for more targeted surveillance to ensure the efficacy of mitigation actions.

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