Cargando…

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

BACKGROUND: Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome...

Descripción completa

Detalles Bibliográficos
Autores principales:	Erkes, Annett, Grove, René P., Žarković, Milena, Krautwurst, Sebastian, Koebnik, Ralf, Morgan, Richard D., Wilson, Geoffrey G., Hölzer, Martin, Marz, Manja, Boch, Jens, Grau, Jan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2023
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10045945/ https://www.ncbi.nlm.nih.gov/pubmed/36973643 http://dx.doi.org/10.1186/s12864-023-09228-1

Ejemplares similares

AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences
por: Grau, Jan, et al.
Publicado: (2016)

Evolution of Transcription Activator-Like Effectors in Xanthomonas oryzae
por: Erkes, Annett, et al.
Publicado: (2017)

Functional analysis of African Xanthomonas oryzae pv. oryzae TALomes reveals a new susceptibility gene in bacterial leaf blight of rice
por: Tran, Tuan T., et al.
Publicado: (2018)

Transcriptional Reprogramming of Rice Cells by Xanthomonas oryzae TALEs
por: Mücke, Stefanie, et al.
Publicado: (2019)

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
por: Viehweger, Adrian, et al.
Publicado: (2019)

Genetic Structure and TALome Analysis Highlight a High Level of Diversity in Burkinabe Xanthomonas Oryzae pv. oryzae Populations
por: Diallo, A., et al.
Publicado: (2023)

Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples
por: Spangenberg, Jannes, et al.
Publicado: (2023)

Integrating Science on Xanthomonas and Xylella for Integrated Plant Disease Management
por: Costa, Joana, et al.
Publicado: (2022)

PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting
por: Erkes, Annett, et al.
Publicado: (2019)

Epigenetic features improve TALE target prediction
por: Erkes, Annett, et al.
Publicado: (2021)

Oxford nanopore technologies—a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella
por: Thomas, Christine, et al.
Publicado: (2023)

The Role of Non-Coding RNAs in the Human Placenta
por: Žarković, Milena, et al.
Publicado: (2022)

Extensive Genomic Rearrangements along with Distinct Mobilome and TALome are Associated with Extreme Pathotypes of a Rice Pathogen
por: Kaur, Amandeep, et al.
Publicado: (2020)

Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas
por: Jacobs, Jonathan M., et al.
Publicado: (2015)

Draft Genome Sequences of Two Xanthomonas euvesicatoria Strains from the Balkan Peninsula
por: Vancheva, Taca, et al.
Publicado: (2015)

Draft Genome Sequences of Two Xanthomonas vesicatoria Strains from the Balkan Peninsula
por: Vancheva, Taca, et al.
Publicado: (2015)

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
por: Jain, Miten, et al.
Publicado: (2016)

Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14‐inducing TAL effectors
por: Blanvillain‐Baufumé, Servane, et al.
Publicado: (2016)

Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
por: Jain, Miten, et al.
Publicado: (2016)

Clustered Regularly Interspaced Short Palindromic Repeats in Xanthomonas citri—Witnesses to a Global Expansion of a Bacterial Pathogen over Time
por: Bellanger, Ninon, et al.
Publicado: (2022)

Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon
por: Fuesslin, Valeria, et al.
Publicado: (2022)

De novo genome assembly resolving repetitive structures enables genomic analysis of 35 European Mycoplasmopsis bovis strains
por: Triebel, Sandra, et al.
Publicado: (2023)

Effector Mimics and Integrated Decoys, the Never-Ending Arms Race between Rice and Xanthomonas oryzae
por: Zuluaga, Paola, et al.
Publicado: (2017)

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis
por: Linde, Jörg, et al.
Publicado: (2023)

Assessing the performance of the Oxford Nanopore Technologies MinION
por: Laver, T., et al.
Publicado: (2015)

Oxford Nanopore MinION Sequencing and Genome Assembly
por: Lu, Hengyun, et al.
Publicado: (2016)

Oxford Nanopore sequencing: new opportunities for plant genomics?
por: Dumschott, Kathryn, et al.
Publicado: (2020)

Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?
por: Kerkhof, Lee J
Publicado: (2021)

Optimized use of Oxford Nanopore flowcells for hybrid assemblies
por: Lipworth, Samuel, et al.
Publicado: (2020)

Application of Oxford Nanopore Technology to Plant Virus Detection
por: Liefting, Lia W., et al.
Publicado: (2021)

De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
por: Hölzer, Martin, et al.
Publicado: (2019)

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”
por: Hölzer, Martin, et al.
Publicado: (2017)

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
por: Brandt, Christian, et al.
Publicado: (2021)

Performance of neural network basecalling tools for Oxford Nanopore sequencing
por: Wick, Ryan R., et al.
Publicado: (2019)

The use of Oxford Nanopore native barcoding for complete genome assembly
por: Bayliss, Sion C, et al.
Publicado: (2017)

Nanocall: an open source basecaller for Oxford Nanopore sequencing data
por: David, Matei, et al.
Publicado: (2017)

Recovery of small plasmid sequences via Oxford Nanopore sequencing
por: Wick, Ryan R., et al.
Publicado: (2021)

A comparison of Oxford nanopore library strategies for bacterial genomics
por: Sauvage, Thomas, et al.
Publicado: (2023)

Corrigendum: poreCov - An Easy to Use, Fast, and Robust Workflow for SARS CoV-2 Genome Reconstruction via Nanopore Sequencing
por: Brandt, Christian, et al.
Publicado: (2022)

Xanthomonas hortorum – beyond gardens: Current taxonomy, genomics, and virulence repertoires
por: Dia, Nay C., et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_f4i06mb2ffjeo8gtuf0ejs96v0