ArticlePlant physiology2004
Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space.
Article in Plant physiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- DNA sequencing technologies: 2006-2016.Nature protocols · 2017Review
- Towards decoding the conifer giga-genome.Plant molecular biology · 2012Review
- 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
- Sequencing and analysis of the gene-rich space of cowpea.BMC genomics · 2008Article
- Sequence-indexed mutations in maize using the UniformMu transposon-tagging population.BMC genomics · 2007Article
- Triticeae genomics: advances in sequence analysis of large genome cereal crops.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2007Review
- Uneven chromosome contraction and expansion in the maize genome.Genome research · 2006Article
- Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid.Genetics · 2006Article
- The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.BMC genomics · 2006Article
- High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9.The Plant cell · 2006Article
- The TIGR Maize Database.Nucleic acids research · 2006Article
- Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Structure and architecture of the maize genome.Plant physiology · 2005Article
- Extension of Lander-Waterman theory for sequencing filtered DNA libraries.BMC bioinformatics · 2005Article
- Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries.Genome research · 2005Article
- Genomic analysis of the 12-oxo-phytodienoic acid reductase gene family of Zea mays.Plant molecular biology · 2005Article
- Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Maize (Zea mays) possesses a large, highly repetitive genome, and subsequently a number of reduced-representation sequencing approaches have been used to try and enrich for gene space while eluding difficulties associated with repetitive DNA. This article documents the ability of publicly available maize expressed sequence tag and Genome Survey Sequences (GSSs; many of which were isolated through the use of reduced representation techniques) to recognize and provide coverage of 78 maize full-length cDNAs (FLCs). All 78 FLCs in the dataset were identified by at least three GSSs, indicating that the majority of maize genes have been identified by at least one currently available GSS. Both methyl-filtration and high-Cot enrichment methods provided a 7- to 8-fold increase in gene discovery rates as compared to random sequencing. The available maize GSSs aligned to 75% of the FLC nucleotides used to perform searches, while the expressed sequence tag sequences aligned to 73% of the nucleotides. Our data suggest that at least approximately 95% of maize genes have been tagged by at least one GSS. While the GSSs are very effective for gene identification, relatively few (18%) of the FLCs are completely represented by GSSs. Analysis of the overlap of coverage and bias due to position within a gene suggest that RescueMu, methyl-filtration, and high-Cot methods are at least partially nonredundant.
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