ArticleNucleic acids research2010
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 39 citations in OpenAlex.
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- Transposable elements: multifunctional players in the plant genome.Frontiers in plant science · 2023Review
- TEMM: A Curated Data Resource for Transposon Element-Based Molecular Markers in Plants.Methods in molecular biology (Clifton, N.J.) · 2023Article
- GrainGenes: a data-rich repository for small grains genetics and genomics.Database : the journal of biological databases and curation · 2022Article
- Development of molecular markers based on LTR retrotransposon in the Cleistogenes songorica genome.Journal of applied genetics · 2022Article
- Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.).Molecular biology reports · 2020Article
- Retro-ElementFrontiers in genetics · 2020Article
- Transcriptome sequencing of Himalayan Raspberry (3 Biotech · 2019Article
- Towards reducing the immunogenic potential of wheat flour: omega gliadins encoded by the D genome of hexaploid wheat may also harbor epitopes for the serious food allergy WDEIA.BMC plant biology · 2018Article
- Generation of a Maize B Centromere Minimal Map Containing the Central Core Domain.G3 (Bethesda, Md.) · 2015Article
- Development of a D genome specific marker resource for diploid and hexaploid wheat.BMC genomics · 2015Article
- Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.Nucleic acids research · 2014Article
- Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays.Heredity · 2013Article
- Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region.Molecular genetics and genomics : MGG · 2012Article
- Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii.BMC genomics · 2012Article
- Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean.The Plant cell · 2012Article
- Characterizing the walnut genome through analyses of BAC end sequences.Plant molecular biology · 2012Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TE) exist in the genomes of nearly all eukaryotes. TE mobilization through 'cut-and-paste' or 'copy-and-paste' mechanisms causes their insertions into other repetitive sequences, gene loci and other DNA. An insertion of a TE commonly creates a unique TE junction in the genome. TE junctions are also randomly distributed along chromosomes and therefore useful for genome-wide marker development. Several TE-based marker systems have been developed and applied to genetic diversity assays, and to genetic and physical mapping. A software tool 'RJPrimers' reported here allows for accurate identification of unique repeat junctions using BLASTN against annotated repeat databases and a repeat junction finding algorithm, and then for fully automated high-throughput repeat junction-based primer design using Primer3 and BatchPrimer3. The software was tested using the rice genome and genomic sequences of Aegilops tauschii. Over 90% of repeat junction primers designed by RJPrimers were unique. At least one RJM marker per 10 Kb sequence of A. tauschii was expected with an estimate of over 0.45 million such markers in a genome of 4.02 Gb, providing an almost unlimited source of molecular markers for mapping large and complex genomes. A web-based server and a command line-based pipeline for RJPrimers are both available at http://wheat.pw.usda.gov/demos/RJPrimers/.
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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.