ArticleProceedings of the National Academy of Sciences of the United States of America2007
A GeneTrek analysis of the maize genome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 64 citations in OpenAlex.
- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots.PLoS genetics · 2020Article
- Article
- Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (The Plant cell · 2017Article
- Gene Deletion in Barley Mediated by LTR-retrotransposon BARE.Scientific reports · 2017Article
- Comparative Analysis ofFrontiers in plant science · 2016Article
- Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei.Plant molecular biology · 2015Article
- Organization and evolution of transposable elements along the bread wheat chromosome 3B.Genome biology · 2014Article
- First insights into the large genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Ttaditional medicinal plant.International journal of molecular sciences · 2013Article
- The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution.Heredity · 2013Article
- Article
- Reference genome sequence of the model plant Setaria.Nature biotechnology · 2012Article
- iPBS: a universal method for DNA fingerprinting and retrotransposon isolation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces.The Plant cell · 2010Article
- EuGène-maize: a web site for maize gene prediction.Bioinformatics (Oxford, England) · 2010Article
- Genetic and physical fine mapping of Scmv2, a potyvirus resistance gene in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- Distribution, diversity, evolution, and survival of Helitrons in the maize genome.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Detailed analysis of a contiguous 22-Mb region of the maize genome.PLoS genetics · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains approximately 37,000 candidate genes with homologues in other plant species. An additional approximately 5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with approximately 30% of BACs containing no genes. BAC gene density varies from 0 to 7.9 per 100 kb, whereas most gene islands contain only one gene. The average number of genes per gene island is 1.7. Only 72% of these genes show collinearity with the rice genome. Particular LTR retrotransposon families (e.g., Gyma) are enriched on gene-free BACs, most of which do not come from pericentromeres or other large heterochromatic regions. Gene-containing BACs are relatively enriched in different families of LTR retrotransposons (e.g., Ji). Two major bursts of LTR retrotransposon activity in the last 2 million years are responsible for the large size of the maize genome, but only the more recent of these is well represented in gene-containing BACs, suggesting that LTR retrotransposons are more efficiently removed in these domains. The results demonstrate that sample sequencing and careful annotation of a few randomly selected BACs can provide a robust description of a complex plant genome.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.