ArticleGenetics2004
Genomic duplication, fractionation and the origin of regulatory novelty.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 1 of them a synthesis that pooled it.
What it found
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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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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.
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Who cites it
95 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Dissection of Leaf Angle Variation in Maize through Genetic Mapping and Meta-Analysis.The plant genome · 2019Pooled it
- A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae).G3 (Bethesda, Md.) · 2026Article
- Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes.Genome biology and evolution · 2026Article
- Evolutionary diversification and immunoprofiling of cathepsin L toolkit in common carp.Frontiers in cellular and infection microbiology · 2026Article
- Genomes from 117 vertebrate species reveal rapidly evolving segmental duplication landscapes.bioRxiv : the preprint server for biology · 2025Article
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Review
- Genome organization and botanical diversity.The Plant cell · 2024Review
- LocoGSE, a sequence-based genome size estimator for plants.Frontiers in plant science · 2024Article
- Dynamics ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- OAF is a DAF-like gene that controls ovule development in plants.Communications biology · 2023Article
- Review
- Evolution and diversification of the O-methyltransferase (OMT) gene family in Solanaceae.Genetics and molecular biology · 2023Article
- Phylogenomic analysis provides insights intoFrontiers in plant science · 2023Article
- Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.Systematic biology · 2022Article
- Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis.PLoS genetics · 2022Article
- Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues.G3 (Bethesda, Md.) · 2022Article
- Chromosome evolution and the genetic basis of agronomically important traits in greater yam.Nature communications · 2022Article
- All Ways Lead to Rome-Meiotic Stabilization Can Take Many Routes in Nascent Polyploid Plants.Genes · 2022Review
- Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish.Nature genetics · 2021Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Having diverged 50 MYA, rice remained diploid while the maize lineage became tetraploid and then fractionated by losing genes from one or the other duplicate region. We sequenced and annotated 13 maize genes (counting the duplicate gene as one gene) on one or the other of the pair of homeologous maize regions; 12 genes were present in one cluster in rice. Excellent maize-rice synteny was evident, but only after the fractionated maize regions were condensed onto a finished rice map. Excluding the gene we used to define homeologs, we found zero retention. Once retained, fractionation (loss of functioning DNA sequence) could occur within cis-acting gene space. We chose a retained duplicate basic leucine zipper transcription factor gene because it was well marked with big, exact phylogenetic footprints (CNSs). Detailed alignments of lg2 and retained duplicate lrs1 to their rice ortholog found that fractionation of conserved noncoding sequences (CNSs) was rare, as expected. Of 30 CNSs, 27 were conserved. The 3 unexpected, missing CNSs and a large insertion support subfunctionalization as a reflection of fractionation of cis-acting gene space and the recent evolution of lg2's novel maize leaf and shoot developmental functions. In general, the principles of fractionation and consolidation work well in making sense of maize gene and genomic sequence data.
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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.