ArticleBMC genomics2017
Comparative analysis of targeted long read sequencing approaches for characterization of a plant's immune receptor repertoire.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight.Biology direct · 2024Article
- Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads.Ecology and evolution · 2023Article
- Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq.BMC genomics · 2022Article
- An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development.Genome biology · 2022Article
- NLR diversity and candidate fusiform rust resistance genes in loblolly pine.G3 (Bethesda, Md.) · 2022Article
- Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification ofLife (Basel, Switzerland) · 2021Article
- Review
- Best practices on the differential expression analysis of multi-species RNA-seq.Genome biology · 2021Review
- Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.).BMC genomics · 2020Article
- BLAST-QC: automated analysis of BLAST results.Environmental microbiome · 2020Article
- Variation Patterns of NLR Clusters inPlant communications · 2020Article
- ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms.Nature communications · 2020Article
- Plant NLR-triggered immunity: from receptor activation to downstream signaling.Current opinion in immunology · 2020Review
- CRISPR-Cas9 enrichment and long read sequencing for fine mapping in plants.Plant methods · 2020Article
- Innovation in Nucleotide-Binding Oligomerization-Like Receptor and Toll-Like Receptor Sensing Drives the Major Histocompatibility Complex-II Free Atlantic Cod Immune System.Frontiers in immunology · 2020Article
- Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.PLoS genetics · 2020Article
- Population Genomic Approaches for Weed Science.Plants (Basel, Switzerland) · 2019Review
- Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria.Scientific reports · 2019Article
- Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology.Plants (Basel, Switzerland) · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified.
resultsSequence yields per MinION run are lower than Illumina, making targeted resequencing an efficient approach. While MinION generates long reads similar to PacBio it doesn't generate the highly accurate multipass consensus reads, which presents downstream bioinformatics challenges. Here we demonstrate how MinION data can be used for RenSeq achieving similar results to the PacBio and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline.
conclusionThe described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.