ArticleProceedings of the National Academy of Sciences of the United States of America2005
Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Linked read technology for assembling large complex and polyploid genomes.BMC genomics · 2018Article
- MaizeThe Plant cell · 2017Article
- The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase.The Plant journal : for cell and molecular biology · 2015Article
- Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan.BMC genomics · 2014Article
- BARREN STALK FASTIGIATE1 is an AT-hook protein required for the formation of maize ears.The Plant cell · 2011Article
- POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.International journal of plant genomics · 2011Article
- MaizeGDB: curation and outreach go hand-in-hand.Database : the journal of biological databases and curation · 2011Article
- Genome wide analyses reveal little evidence for adaptive evolution in many plant species.Molecular biology and evolution · 2010Article
- 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
- Article
- Rare genetic variation at Zea mays crtRB1 increases beta-carotene in maize grain.Nature genetics · 2010Article
- High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing.Genetics · 2010Article
- Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.Genome biology · 2010Article
- Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome.PLoS genetics · 2009Article
- Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize.Plant physiology · 2009Article
- Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing.BMC genomics · 2009Article
- Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize.Genes & development · 2009Article
- Article
- Advancing cell biology and functional genomics in maize using fluorescent protein-tagged lines.Plant physiology · 2009Article
- MaizeGDB becomes 'sequence-centric'.Database : the journal of biological databases and curation · 2009Article
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7 authors.
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Abstract
Recent sequencing efforts have targeted the gene-rich regions of the maize (Zea mays L.) genome. We report the release of an improved assembly of maize assembled genomic islands (MAGIs). The 114,173 resulting contigs have been subjected to computational and physical quality assessments. Comparisons to the sequences of maize bacterial artificial chromosomes suggest that at least 97% (160 of 165) of MAGIs are correctly assembled. Because the rates at which junction-testing PCR primers for genomic survey sequences (90-92%) amplify genomic DNA are not significantly different from those of control primers ( approximately 91%), we conclude that a very high percentage of genic MAGIs accurately reflect the structure of the maize genome. EST alignments, ab initio gene prediction, and sequence similarity searches of the MAGIs are available at the Iowa State University MAGI web site. This assembly contains 46,688 ab initio predicted genes. The expression of almost half (628 of 1,369) of a sample of the predicted genes that lack expression evidence was validated by RT-PCR. Our analyses suggest that the maize genome contains between approximately 33,000 and approximately 54,000 expressed genes. Approximately 5% (32 of 628) of the maize transcripts discovered do not have detectable paralogs among maize ESTs or detectable homologs from other species in the GenBank NR nucleotide/protein database. Analyses therefore suggest that this assembly of the maize genome contains approximately 350 previously uncharacterized expressed genes. We hypothesize that these "orphans" evolved quickly during maize evolution and/or domestication.
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