ArticleGenome research2005
Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 66 citations in OpenAlex.
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- Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.Nucleic acids research · 2018Review
- Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Molecular breeding : new strategies in plant improvement · 2016Article
- Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS).Frontiers in plant science · 2015Article
- Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea.BMC genomics · 2014Article
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- SNP markers and their impact on plant breeding.International journal of plant genomics · 2012Article
- Spreading of heterochromatin is limited to specific families of maize retrotransposons.PLoS genetics · 2012Article
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- Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- Genome-wide distribution of transposed Dissociation elements in maize.The Plant cell · 2010Article
- Rapid genomic characterization of the genus vitis.PloS one · 2010Article
- Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean.The Plant cell · 2010Article
- A single molecule scaffold for the maize genome.PLoS genetics · 2009Article
- Advances in maize genomics and their value for enhancing genetic gains from breeding.International journal of plant genomics · 2009Article
- Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains.BMC genomics · 2008Article
- Display of a maize cDNA library on baculovirus infected insect cells.BMC biotechnology · 2008Article
- Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes.PloS one · 2007Article
- An improved method to identify BAC clones using pooled overgos.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A new technology was developed to assist gene-enrichment sequencing of any complex plant genome, employing maize as the test organism. Hypomethylated partial restriction (HMPR) libraries were constructed by using independent partial digestions with methylation-sensitive restriction enzymes HpaII (5'-CCGG-3') and HpyCH4IV (5'-ACGT-3'). Fragments of 1-4 kb were purified and cloned, followed by sequence analysis of >2000 clones from 10 separate libraries. Organellar clones comprised approximately 10% of each library but were useful in showing that no chimeric clones were generated and that digestion efficiencies were 10%-25% in different libraries. Four separate HMPR libraries, analyzed in detail, exhibited very similar degrees of gene enrichment and repeat depletion. Known gene homologies were found in approximately 25% of the HMPR clones, compared with <4% in clones from a fully random set of unfiltered maize shotgun sequences. This six- to sevenfold enrichment for genes compares favorably with the best previous gene enrichment techniques in maize, High Cot analysis and methylation filtration. Compared with High Cot and methylation filtration, HMPR is exceptional in depleting retrotransposons' content to the lowest level yet observed (<5%, compared with >70% for unfiltered maize sequences) and in providing an unmatched enrichment for the "unknown" sequences that contain promoters, introns, and other gene-adjacent regions.
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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.