scholarly journals High-Quality Genome Resource of the Pathogen of Diaporthe (Phomopsis) phragmitis Causing Kiwifruit Soft Rot

2020 ◽  
Author(s):  
Pu Liu ◽  
Wang Xiaojie ◽  
Dong Hongjie ◽  
Jianbin Lan ◽  
Kuan Liang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Fruit Rot ◽  
Economic Plant ◽  
High Quality ◽  
Total Size ◽  
Genome Wide ◽  
Solid Foundation ◽  
High Quality Genome

Diaporthe spp. are critical plant pathogens that cause wood cankers, wilt, dieback, and fruit rot in a wide variety of economic plant hosts and are regarded as one of the most acute threats faced by kiwifruit industry worldwide. Diaporthe phragmitis strain NJD1 is a highly pathogenic isolate of soft rot of kiwifruit. Here, we present a high-quality genome-wide sequence of D. phragmitis NJD1 that was assembled into 28 contigs containing a total size of 58.33 Mb and N50 length of 3.55 Mb. These results lay a solid foundation for understanding host–pathogen interaction and improving disease management strategies.

scholarly journals High-Quality Genome Resource of the Pathogen of Botryosphaeria dothidea Causing Kiwifruit Soft Rot

2021 ◽  
pp. PHYTOFR-07-20-0
Author(s):  
Kuan Liang ◽  
Jianbin Lan ◽  
Baoquan Wang ◽  
Yuanyuan Liu ◽  
Qi Lu ◽  
...  
Keyword(s):  
De Novo ◽  
Gc Content ◽  
Soft Rot ◽  
Read Length ◽  
Comparative Genomic ◽  
Secretory Proteins ◽  
Botryosphaeria Dothidea ◽  
High Quality ◽  
Total Size ◽  
High Quality Genome

Kiwifruit soft rot caused by the fungal pathogen Botryosphaeria dothidea is a serious disease in kiwifruit-growing regions worldwide. In this study, we reported the high-quality genome sequence of the highly virulent B. dothidea strain PTZ1 using PacBio Sequel techniques. In total, 100.87 million clean reads with mean read length of 9,871 bp were obtained. De novo assembly resulted in 28 contigs with a total size of 44.45 Mb. The GC content of the genome was 54.59%. Furthermore, genes related to specific virulence of the strain were identified, including 259 fungal cytochrome P450s, 550 carbohydrate-active enzymes, 860 secretory proteins, and 1,182 pathogen–host interactions related proteins. The genome is a useful resource to serve as a reference to facilitate the analysis of B. dothidea isolates and comparative genomic studies of the necrotroph pathogens. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Long Fragment Read (LFR) Technology: Cost-Effective, High-Quality Genome-Wide Molecular Haplotyping

2017 ◽  
pp. 191-205 ◽  
Author(s):  
Mark A. McElwain ◽  
Rebecca Yu Zhang ◽  
Radoje Drmanac ◽  
Brock A. Peters
Keyword(s):  
Cost Effective ◽  
High Quality ◽  
Genome Wide ◽  
High Quality Genome ◽  
Long Fragment Read

scholarly journals Genome sequence resource for the plant pathogen Sclerotinia sclerotiorum WH6 isolated in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Xiong Zhang ◽  
Xiaohui Cheng ◽  
Lijiang Liu ◽  
Shengyi Liu
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Genome Sequence ◽  
Fungal Pathogen ◽  
Sclerotinia Stem Rot ◽  
High Quality ◽  
Total Size ◽  
Host Interactions ◽  
A Genome ◽  
The World ◽  
High Quality Genome

Sclerotinia sclerotiorum is a notorious fungal pathogen that causes sclerotinia stem rot (SSR) on many important crops in China and worldwide. Here, we present a high- quality genome assembly of S. sclerotiorum strain WH6 using the PacBio SMRT cell platform. The assembled genome has a total size of 38.96 Mbp, with a contig N50 length of 1.90 Mbp, and encodes 10,512 predicted coding genes, including 685 secreted proteins and 65 effector candidates. This is the the first report of a genome sequence from China. The WH6 genome sequence provides a valuable resource for facilitating our understanding of S. sclerotiorum-host interactions and SSR control in China and the world.

scholarly journals Genome Sequence of Fusarium oxysporum f. sp. conglutinans, the Etiological Agent of Cabbage Fusarium Wilt

2020 ◽  
pp. MPMI-08-20-0245
Author(s):  
Fangwei Yu ◽  
Wei Zhang ◽  
Shenyun Wang ◽  
Hong Wang ◽  
Li Yu ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
Genome Sequence ◽  
High Quality ◽  
Total Size ◽  
Protein Coding ◽  
Long Read ◽  
Race 1 ◽  
High Quality Genome ◽  
Open Access Article

Fusarium oxysporum f. sp. conglutinans is the causal agent of Fusarium wilt of cabbage (Brassica oleracea var. capitata L.), which results in severe yield loss. Here, we report a high-quality genome sequence of a race 1 strain (IVC-1) of F. oxysporum f. sp. conglutinans, which was assembled using a combination of PacBio long-read and Illumina short-read sequences. The assembled IVC-1 genome has a total size of 71.18 Mb, with a contig N50 length of 4.59 Mb, and encodes 23,374 predicted protein-coding genes. The high-quality genome of IVC-1 provides a valuable resource for facilitating our understanding of F. oxysporum f. sp. conglutinans–cabbage interaction. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Heart Rot of Pomegranate: Disease Etiology and the Events Leading to Development of Symptoms

Plant Disease ◽  
2015 ◽  
Vol 99 (4) ◽  
pp. 496-501 ◽  
Author(s):  
David Ezra ◽  
Benny Kirshner ◽  
Michal Hershcovich ◽  
Dani Shtienberg ◽  
Itzhak Kosto
Keyword(s):  
Fruit Development ◽  
Management Strategies ◽  
Soft Rot ◽  
Fruit Rot ◽  
Black Rot ◽  
Causative Pathogen ◽  
Disease Etiology ◽  
Rot Disease ◽  
Pomegranate Fruit ◽  
Organ Colonization

Pomegranate fruit rot disease, known as “heart rot” or “black heart,” is a major pomegranate disease that impacts production worldwide. Heart rot is characterized by black rot of the fruit core that spreads from the calyx area, whereas the outer peel and the hard rind retain their healthy appearance. Aims of the present study were to identify the pathogen that causes pomegranate heart rot in Israel and to study the dynamics of fruit-organ colonization by fungi during fruit development, as the first steps toward the development of management strategies. Several fungi were isolated from pomegranate fruits, among which were species of Penicillium, Aspergillus, Botrytis, and Rhizopus, but the causative pathogen of the disease was identified as Alternaria alternata. This fungus was isolated from the pistils of more than 85% of open flowers and ∼20% of the loculi of asymptomatic fruits and from all tissues of the symptomatic fruits. The dynamics of fruit-organ colonization by fungi during fruit development was recorded in six commercial orchards in 2010 and 2011. It was found that A. alternata spores germinate on the stigmata of open flowers and develop into the style. In some fruits, the mycelium grows into the tunnel and reaches the lower loculus, where the fungus becomes latent for about 3 to 4 months pending initiation of fruit ripening. Then, in a small number of fruits, the fungus starts growing and invades the arils, causing black rot of the arils in the lower loculus. At the beginning of disease development, the fungus causes brown soft rot of the arils, which becomes black and dry as the fungus grows. Eventually, the fungus grows from the lower loculus into the upper loculi, causing rot of the entire fruit.

scholarly journals Genomic Characterization, Formulation and Efficacy in Planta of a Siphoviridae and Podoviridae Protection Cocktail against the Bacterial Plant Pathogens Pectobacterium spp.

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 150
Author(s):  
Maja A. Zaczek-Moczydłowska ◽  
Gillian K. Young ◽  
James Trudgett ◽  
Colin C. Fleming ◽  
Katrina Campbell ◽  
...  
Keyword(s):  
Crop Production ◽  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Field Trials ◽  
Control Measures ◽  
In Planta ◽  
Sustainable Food ◽  
Phage Cocktail ◽  
Causative Agents

In the face of global human population increases, there is a need for efficacious integrated pest management strategies to improve agricultural production and increase sustainable food production. To counteract significant food loses in crop production, novel, safe and efficacious measures should be tested against bacterial pathogens. Pectobacteriaceae species are one of the causative agents of the bacterial rot of onions ultimately leading to crop losses due to ineffective control measures against these pathogens. Therefore, the aim of this study was to isolate and characterize bacteriophages which could be formulated in a cocktail and implemented in planta under natural environmental conditions. Transmission electron microscopy (TEM) and genome analysis revealed Siphoviridae and Podoviridae family bacteriophages. To test the protective effect of a formulated phage cocktail against soft rot disease, three years of field trials were performed, using three different methods of treatment application. This is the first study to show the application of a phage cocktail containing Podoviridae and Siphoviridae bacteriophages capable of protecting onions against soft rot in field conditions.

scholarly journals High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

PLoS ONE ◽  
2019 ◽  
Vol 14 (6) ◽  
pp. e0210928 ◽  
Author(s):  
Stijn Vanderzande ◽  
Nicholas P. Howard ◽  
Lichun Cai ◽  
Cassia Da Silva Linge ◽  
Laima Antanaviciute ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
High Quality ◽  
Genome Wide ◽  
High Quality Genome

scholarly journals Complete Genome Sequence Resource for Xanthomonas fragariae Causing Crown Infection Pockets in Strawberry

2021 ◽  
Author(s):  
Feng Wei ◽  
Danjuan Wang ◽  
Sihao Fan ◽  
Jiancheng Shi ◽  
Xiaolin Cai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Host Adaptation ◽  
Pathological Process ◽  
High Quality ◽  
Leaf Spots ◽  
Xanthomonas Fragariae ◽  
Quarantine Pathogen ◽  
High Quality Genome

Xanthomonas fragariae (X. fragariae ) is a global quarantine pathogen, which typically inflicting angular leaf spots. In the present study, we report a new 4.11 Mb high-quality genome sequence of X. fragariae YL19. YL19 can make the strawberry plants have the typical angular leaf spot symptom and have crown infection pockets symptom in China. This new symptom has not been reported in other X. fragariae. Compared with typical X. fragariae strains, including PD885, NBC2815, PD5205, Fap21, and Fap29, the genome and plasmid in YL19 were smaller in size, which lacked 109 coding genes and has more CAZymes genes and secondary metabolism genes. The YL19 genome ought to clarify the molecular mechanisms of genome evolution, host adaptation, and pathological process of X. fragariae and the improvement of strawberry management strategies.

scholarly journals High-Quality Genome Resource of Clonostachys rosea strain CanS41 by Oxford Nanopore Long-Read Sequencing

Plant Disease ◽  
2021 ◽  
Author(s):  
Haoming Wang ◽  
Yongrong Dong ◽  
Weixue Liao ◽  
Xin Zhang ◽  
Qinhu Wang ◽  
...  
Keyword(s):  
Biological Control ◽  
Genome Assembly ◽  
Plant Pathogens ◽  
Gene Annotation ◽  
Gc Content ◽  
Clonostachys Rosea ◽  
High Quality ◽  
Fungal Plant Pathogens ◽  
Oxford Nanopore ◽  
High Quality Genome

Clonostachys rosea is a necrotrophic mycoparasitic fungus with excellent biological control ability against numerous fungal plant pathogens. Here, we performed genomic sequencing of C. rosea strain CanS41 using Oxford Nanopore sequencing technology. We generated a high-quality genome assembly (>99.99% accuracy), which comprised 26 contigs containing 60.68 Mb sequences with a GC content of 48.55% and a repeat content of 8.38%. The N50 contig length is 3.02 Mb. In total, 20,818 protein-coding genes were identified and functionally annotated. Genes encoding secreted proteins and carbohydrate-active enzymes as well as secondary metabolic gene clusters were also identified and analyzed. In summary, the high-quality genome assembly and gene annotation provided here will allow further exploration of biological functions and enhance biological control ability of C. rosea.

scholarly journals High-Quality Genome Sequence Resource for Fusarium andiyazi Causing Pokkah Boeng Disease of Sugarcane in China

2021 ◽  
Author(s):  
Yixue Bao ◽  
Kaiyuan Pan ◽  
Khan Muhammad Tahir ◽  
Baoshan Chen ◽  
MUQING ZHANG
Keyword(s):  
Fusarium Species ◽  
Gc Content ◽  
Effector Proteins ◽  
High Quality ◽  
Total Size ◽  
Host Interactions ◽  
Pokkah Boeng ◽  
Oxford Nanopore ◽  
New Varieties ◽  
High Quality Genome

Sugarcane pokkah boeng disease (PBD) is emerging as a prevalent foliar disease in China. This airborne disease is caused by the Fusarium species complex. To investigate the diversity and evolution of Fusarium species, we performed the whole-genome sequencing of Fusarium andiyazi YN28 using a combination of the Oxford Nanopore and the Illumina technology. The F. andiyazi YN28 genome was sequenced, assembled, and annotated. A high-quality genome was assembled into 24 contigs with an N50 of 2.80 Mb. The genome assembly generated a total size of 44.1 Mb with a GC content of 47.64%. A total of 15,508 genes were predicted, including 794 genes related to the carbohydrate-active enzymes, 397 ncRNAs, 155 genes associated with transporter classification, 4,550 genes linked to pathogen-host interactions, and 269 genes involved in effector proteins. Collectively, our results will provide insight into the host-pathogen interaction and will facilitate the breeding of new varieties of sugarcane resistant to PBD.

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