Comparative genomics, pangenomics, and phenomic studies of Pectobacterium betavasculorum strains isolated from sugar beet, potato, sunflower, and artichoke: insights into pathogenicity, virulence determinants, and adaptation to the host plant.
Bacteria of genus Pectobacterium, encompassing economically significant pathogens affecting various plants, includes the species P. betavasculorum, initially associated with beetroot infection. However, its host range is much broader. It causes diseases of sunflower, potato, tomato, carrots, sweet potato, radish, squash, cucumber, and chrysanthemum. To explain this phenomenon, a comprehensive pathogenomic and phenomic characterisation of P. betavasculorum species was performed.
Pubmed ID: 38576793 RIS Download
Research resources used in this publication
None foundAdditional research tools detected in this publication
- QUAST (RRID:SCR_001228)
- UniProt (RRID:SCR_002380)
- GenBank (RRID:SCR_002760)
- DOE Joint Genome Institute (RRID:SCR_003045)
- SSPACE (RRID:SCR_005056)
- Geneious (RRID:SCR_010519)
- Velvet (RRID:SCR_010755)
- MUSCLE (RRID:SCR_011812)
- Trimmomatic (RRID:SCR_011848)
- Ray Meta (RRID:SCR_011918)
- PhyloPhlAn (RRID:SCR_013082)
- New England Biolabs (RRID:SCR_013517)
- Pathway Tools (RRID:SCR_013786)
- FastQC (RRID:SCR_014583)
- ggplot2 (RRID:SCR_014601)
- RAST Server (RRID:SCR_014606)
- jModelTest (RRID:SCR_015244)
- GET_HOMOLOGUES (RRID:SCR_015705)
- Centre for Agriculture and Biosciences International (RRID:SCR_016467)
- Porechop (RRID:SCR_016967)
- Flye (RRID:SCR_017016)
- ComplexHeatmap (RRID:SCR_017270)
- Unicycler (RRID:SCR_024380)
Antibodies used in this publication
None foundAssociated grants
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This is a list of tools and resources that we have found mentioned in this publication.
QUAST (tool)
RRID:SCR_001228
Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.
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RRID:SCR_002380
Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.
View all literature mentionsGenBank (tool)
RRID:SCR_002760
NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
View all literature mentionsDOE Joint Genome Institute (tool)
RRID:SCR_003045
Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
View all literature mentionsSSPACE (tool)
RRID:SCR_005056
A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.
View all literature mentionsGeneious (tool)
RRID:SCR_010519
Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
View all literature mentionsVelvet (tool)
RRID:SCR_010755
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux.
View all literature mentionsMUSCLE (tool)
RRID:SCR_011812
Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.
View all literature mentionsTrimmomatic (tool)
RRID:SCR_011848
Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsRay Meta (tool)
RRID:SCR_011918
Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.
View all literature mentionsPhyloPhlAn (tool)
RRID:SCR_013082
Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations.
View all literature mentionsPathway Tools (tool)
RRID:SCR_013786
A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks.
View all literature mentionsFastQC (tool)
RRID:SCR_014583
Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsggplot2 (tool)
RRID:SCR_014601
Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsRAST Server (tool)
RRID:SCR_014606
A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.
View all literature mentionsjModelTest (tool)
RRID:SCR_015244
Software tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests, Akaike and Bayesian information criteria, and a decision theory method. It also provides estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates.
View all literature mentionsGET_HOMOLOGUES (tool)
RRID:SCR_015705
Software package for pan-genome analysis. This software is suitable for bacterial genomes and the study of intra-specific eukaryotic pan-genomes.
View all literature mentionsCentre for Agriculture and Biosciences International (tool)
RRID:SCR_016467
An international not-for-profit organization to solve problems in agriculture and the environment. Specialize in microbial identification and verification, and provide professional microbiology services in support of industry, academia and agriculture. Established by a United Nations.
View all literature mentionsPorechop (tool)
RRID:SCR_016967
Software tool for finding and removing adapters from Oxford Nanopore reads.
View all literature mentionsFlye (tool)
RRID:SCR_017016
Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms.
View all literature mentionsComplexHeatmap (tool)
RRID:SCR_017270
Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.
View all literature mentionsUnicycler (tool)
RRID:SCR_024380
Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.
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