scholarly journals A reference genome sequence resource for the sugar beet root rot pathogen Aphanomyces cochlioides

2021 ◽  
Author(s):  
Jacob Botkin ◽  
Ashok K Chanda ◽  
Frank N Martin ◽  
Cory D Hirsch
Keyword(s):  
Sugar Beet ◽  
Genome Assembly ◽  
Root Rot ◽  
De Novo ◽  
Sequence Data ◽  
Aphanomyces Cochlioides ◽  
Beet Root ◽  
Long Read ◽  
Illumina Sequence ◽  
Sugar Beet Root

Aphanomyces cochlioides, the causal agent of damping-off and root rot of sugar beet (Beta vulgaris L.), is a soil-dwelling oomycete responsible for yield losses in all major sugar beet growing regions. Currently, genomic resources for A. cochlioides are limited. Here we report a de novo genome assembly using a combination of long-read MinION (Oxford Nanopore Technologies) and short-read Illumina sequence data for A. cochlioides isolate 103-1, from Breckenridge, MN. The assembled genome was 76.3 Mb, with a contig N50 of 2.6 Mb. The reference assembly was annotated and was composed of 32.1% repetitive elements and 20,274 gene models. This high-quality genome assembly of A. cochlioides will be a valuable resource for understanding genetic variation, virulence factors, and comparative genomics of this important sugar beet pathogen.

scholarly journals Sugar beet root rot at harvest in the US Intermountain West

2009 ◽  
Vol 31 (2) ◽  
pp. 232-240 ◽  
Author(s):  
Carl A. Strausbaugh ◽  
Anne M. Gillen
Keyword(s):  
Sugar Beet ◽  
Root Rot ◽  
Intermountain West ◽  
Beet Root ◽  
The Us ◽  
Sugar Beet Root

scholarly journals NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Willem de Koning ◽  
Milad Miladi ◽  
Saskia Hiltemann ◽  
Astrid Heikema ◽  
John P Hays ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Bioinformatics Analysis ◽  
De Novo ◽  
Sequence Data ◽  
Ease Of Use ◽  
Easy Access ◽  
Complex Data ◽  
Sequencing Data ◽  
Long Read ◽  
Sequencing Platforms

Abstract Background Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies–based long-read sequencing “nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers. Results The Galaxy platform provides a user-friendly interface to computational command line–based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed “NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads. Conclusions A range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.

scholarly journals Antifungal effect of some plant extracts and their combination with Moncut fungicide on sugar beet root rot

2021 ◽  
Vol 42 (2) ◽  
pp. 162-182
Author(s):  
M.E.H. Osman ◽  
A.M. Abo Shady ◽  
El-Sayed A. B. ◽  
Eman F. Abo ElKheir
Keyword(s):  
Sugar Beet ◽  
Plant Extracts ◽  
Root Rot ◽  
Antifungal Effect ◽  
Beet Root ◽  
Sugar Beet Root

Sugar beet root rot loss: ANN and Regression models

2021 ◽  
Vol 131 ◽  
pp. 126392
Author(s):  
A.S. Eslami ◽  
N. Safaie ◽  
S.B. Mahmoudi ◽  
Sh. Mojerlou
Keyword(s):  
Sugar Beet ◽  
Root Rot ◽  
Regression Models ◽  
Beet Root ◽  
Sugar Beet Root

scholarly journals Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens

2016 ◽  
Vol 106 (1) ◽  
pp. 76-86 ◽  
Author(s):  
Sebastian Liebe ◽  
Daniela S. Christ ◽  
Ralf Ehricht ◽  
Mark Varrelmann
Keyword(s):  
Sugar Beet ◽  
Root Rot ◽  
Plant Pathogens ◽  
Detection Methods ◽  
Penicillium Expansum ◽  
High Yield ◽  
Marker Genes ◽  
Species Differentiation ◽  
Beet Root ◽  
Sugar Beet Root

Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present.

scholarly journals Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG 107.79

2016 ◽  
Author(s):  
Amanda M. Davis ◽  
Manuela Iovinella ◽  
Sally James ◽  
Thomas Robshaw ◽  
Jennifer R. Dodson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Draft Genome ◽  
Carbon Sources ◽  
Red Alga ◽  
Full Genome Sequencing ◽  
Galdieria Sulphuraria ◽  
Long Read

AbstractWe report here the de novo assembly of a eukaryotic genome using only MinION nanopore DNA sequence data by examining a novel Galdieria sulphuraria genome: strain SAG 107.79. This extremophilic red alga was targeted for full genome sequencing as we found that it could grow on a wide variety of carbon sources and could uptake several precious and rare-earth metals, which places it as an interesting biological target for disparate industrial biotechnological uses. Phylogenetic analysis clearly places this as a species of G. sulphuraria. Here we additionally show that the genome assembly generated via nanopore long read data was of a high quality with regards to low total number of contiguous DNA sequences and long length of assemblies. Collectively, the MinION platform looks to rival other competing approaches for de novo genome acquisition with available informatics tools for assembly. The genome assembly is publically released as NCBI BioProject PRJNA330791. Further work is needed to reduce small insertion-deletion errors, relative to short-read assemblies.

scholarly journals Sugarbeet root rot in drought conditions

2005 ◽  
pp. 103-111 ◽  
Author(s):  
Stevan Jasnic ◽  
Vera Stojsin ◽  
Ferenc Bagi
Keyword(s):  
Sugar Beet ◽  
Root Rot ◽  
Weather Conditions ◽  
Macrophomina Phaseolina ◽  
Economic Damage ◽  
Beet Root ◽  
Genus Fusarium ◽  
Leaf Chlorosis ◽  
Sugar Beet Root ◽  
Plant Vitality

In recent years several types of sugarbeet root rot have occurred in our country causing significant economic damage. The most frequent symptoms are leaf chlorosis and brown-black wet necrosis of the root. The necrosis spread through the entire root and vascular strands. In the course of this study F. oxysporum was the most frequently isolated from infected sugar beet roots. The incidence of other fungi (Fusarium solani, Rhizoctonia solani and Macrophomina phaseolina) was much lower and it depended on weather conditions. High temperatures occurring during dry years encourage the development of F. oxysporum, the causer of sugar beet root rot. In 2000, an extremely dry year, plant vitality was satisfactory in the experiment with irrigation and the average root rot incidence was low (2,91%). In the nonirrigated variant the average incidence was high (71,02%). It may be concluded on the basis of the results from five years (2000-2004) that the major causal agents of sugarbeet root rot in our country are species from genus Fusarium, especially F. oxysporum. Fusarium wilt and root rot are due to the increased frequency of dry and warm years.

scholarly journals Bacteria and Yeast Associated with Sugar Beet Root Rot at Harvest in the Intermountain West

Plant Disease ◽  
2008 ◽  
Vol 92 (3) ◽  
pp. 357-363 ◽  
Author(s):  
Carl A. Strausbaugh ◽  
Anne M. Gillen
Keyword(s):  
Sugar Beet ◽  
Root Rot ◽  
Fungal Infections ◽  
Bacterial Species ◽  
Enteric Bacteria ◽  
Beet Root ◽  
Group A ◽  
Sugar Beet Root ◽  
Bacterial Rot ◽  
Group B

An undescribed wet rot of roots was observed in surveys of recently harvested sugar beet roots in Idaho and eastern Oregon in 2004 and 2005. Microorganisms isolated from 287 roots fell into the following groups: A (41% of strains), B (29%), C (17%), D (11%), E (2%), and F (1%). Groups A, B, C, and F were composed of bacteria while groups D and E were yeasts. Subgroup A1 (80% of group A strains) included Leuconostoc mesenteroides subsp. dextranicum strains and subgroup A2 (20%) contained Lactobacillus strains. Group B was dominated by subgroup B1 (92% of strains), which included Gluconobacter strains. When only one organism was isolated from rotted roots, strains from subgroup A1 were isolated most frequently. Group C was composed of enteric bacteria. Strain B322 of L. mesenteroides subsp. dextranicum caused the most severe rot on root slices and produced symptoms similar to those in harvested roots. Results suggest that L. mesenteroides subsp. dextranicum is among the first bacterial species to enter sugar beet roots, closely following fungal infections or entering directly through openings such as growth cracks. The bacterial rot leads to yield loss in the field but likely also leads to storage and factory-processing problems.

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