ArticleProceedings of the National Academy of Sciences of the United States of America2016
Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed, 44 citations in OpenAlex.
- Phylogenomics of Plasmopara halstedii Reveals Genomic Regions Associated With the Breakdown of Sunflower Downy Mildew Resistance Genes.Molecular ecology · 2026Article
- The Fie1-PRC2 complex regulates H3K27me3 deposition to balance endosperm filling and development in cereals.Plant communications · 2025Article
- Editing the 19 kDa alpha-zein gene family generates non-opaque2-based quality protein maize.Plant biotechnology journal · 2024Article
- Article
- Tandem duplicate expression patterns are conserved between maize haplotypes of thePlant direct · 2021Article
- Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau.Scientific reports · 2020Article
- Genomics-Enabled Analysis ofInternational journal of molecular sciences · 2020Article
- Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing ofProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus.Plant direct · 2019Article
- NAC-type transcription factors regulate accumulation of starch and protein in maize seeds.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- High frequency DNA rearrangement atCommunications biology · 2019Article
- Modelling BioNano optical data and simulation study of genome map assembly.Bioinformatics (Oxford, England) · 2018Article
- Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.Nature genetics · 2018Article
- Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time.G3 (Bethesda, Md.) · 2018Article
- Overexpression of serine acetyltransferase in maize leaves increases seed-specific methionine-rich zeins.Plant biotechnology journal · 2018Article
- Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat.Scientific reports · 2018Article
- Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.Nature genetics · 2018Article
- Gene Duplication and Evolution Dynamics in the Homeologous Regions Harboring Multiple Prolamin and Resistance Gene Families in Hexaploid Wheat.Frontiers in plant science · 2018Article
- Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association ofFrontiers in plant science · 2018Article
- Uniparental and transgressive expression of α-zeins in maize endosperm of o2 hybrid lines.PloS one · 2018Article
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
Haplotype variation not only involves SNPs but also insertions and deletions, in particular gene copy number variations. However, comparisons of individual genomes have been difficult because traditional sequencing methods give too short reads to unambiguously reconstruct chromosomal regions containing repetitive DNA sequences. An example of such a case is the protein gene family in maize that acts as a sink for reduced nitrogen in the seed. Previously, 41-48 gene copies of the alpha zein gene family that spread over six loci spanning between 30- and 500-kb chromosomal regions have been described in two Iowa Stiff Stalk (SS) inbreds. Analyses of those regions were possible because of overlapping BAC clones, generated by an expensive and labor-intensive approach. Here we used single-molecule real-time (Pacific Biosciences) shotgun sequencing to assemble the six chromosomal regions from the Non-Stiff Stalk maize inbred W22 from a single DNA sequence dataset. To validate the reconstructed regions, we developed an optical map (BioNano genome map; BioNano Genomics) of W22 and found agreement between the two datasets. Using the sequences of full-length cDNAs from W22, we found that the error rate of PacBio sequencing seemed to be less than 0.1% after autocorrection and assembly. Expressed genes, some with premature stop codons, are interspersed with nonexpressed genes, giving rise to genotype-specific expression differences. Alignment of these regions with those from the previous analyzed regions of SS lines exhibits in part dramatic differences between these two heterotic groups.
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.