ArticlePLoS genetics2009
Detailed analysis of a contiguous 22-Mb region of the maize genome.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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.
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Who cites it
26 citing papers in PubMed, 49 citations in OpenAlex.
- Article
- Quadruplex-Forming Motif Inserted into 3'UTR ofBiology · 2021Article
- Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks.Genes · 2020Article
- Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids.Plant physiology · 2020Article
- PmiRExAt: plant miRNA expression atlas database and web applications.Database : the journal of biological databases and curation · 2016Article
- A gain-of-function Bushy dwarf tiller 1 mutation in rice microRNA gene miR156d caused by insertion of the DNA transposon nDart1.Scientific reports · 2015Article
- Article
- Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.The Plant journal : for cell and molecular biology · 2014Article
- Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome.PLoS genetics · 2014Article
- The barley Frost resistance-H2 locus.Functional & integrative genomics · 2014Article
- Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.Genome research · 2013Article
- Efficient known ncRNA search including pseudoknots.BMC bioinformatics · 2013Article
- A physical map of the short arm of wheat chromosome 1A.PloS one · 2013Article
- Insular organization of gene space in grass genomes.PloS one · 2013Article
- Pod corn is caused by rearrangement at the Tunicate1 locus.The Plant cell · 2012Article
- Evolution and expression of tandem duplicated maize flavonol synthase genes.Frontiers in plant science · 2012Article
- MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.BMC bioinformatics · 2011Article
- A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat.Plant physiology · 2011Article
- miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
55 authors at 15 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
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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.