Reference health
Insights from the Comparison of Plant Genome Sequences
2 of 144 checkable references need attention · checked 2026-07-22
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
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References needing attention
does not resolve to a known work10.1101/gr.229202. Article published online before March 2002
does not resolve to a known work10.1101/gr.221802. Article published online before print in April 2002
The 142 checked references that resolve
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Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing
resolves10.1534/genetics.104.033522
Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid
resolves10.1038/nature05230
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
resolves10.1016/j.gde.2005.09.010
Transposable elements, gene creation and genome rearrangement in flowering plants
resolves10.1105/tpc.106.049338
The Gene Balance Hypothesis: From Classical Genetics to Modern Genomics
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Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes[W]
resolves10.1534/genetics.109.101998
Identification of EMS-Induced Mutations in
<i>Drosophila melanogaster</i>
by Whole-Genome Sequencing
resolves10.1073/pnas.0502365102
Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses
resolves10.1038/nature01521
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
resolves10.1093/molbev/msl049
Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes
resolves10.1093/bioinformatics/btg1008
Fast identification and statistical evaluation of
segmental homologies in comparative maps
resolves10.1186/gb-2003-4-10-r68
DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization
resolves10.1073/pnas.0507782103
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication
resolves10.1093/nar/gkj123
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
resolves10.1371/journal.pone.0000383
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes
resolves10.1101/gad.11.16.2124
Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance
resolves10.1073/pnas.94.7.3442
Transcriptional analysis of nucleolar dominance in polyploid plants: Biased expression/silencing of progenitor rRNA genes is developmentally regulated in
<i>Brassica</i>
resolves10.1371/journal.pbio.1000112
Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
resolves10.1126/science.1138632
Common Sequence Polymorphisms Shaping Genetic Diversity in
<i>Arabidopsis thaliana</i>
resolves10.1105/tpc.12.9.1551
Phenotypic Instability and Rapid Gene Silencing in Newly Formed Arabidopsis Allotetraploids
resolves10.1073/pnas.0308127100
Darwin's abominable mystery: Insights from a supertree of the angiosperms
resolves10.1007/s001220050026
Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice
resolves10.1007/s10577-009-9055-9
Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes
resolves10.1104/pp.62.2.185
A Comparison of Photosynthetic Characteristics of <i>Encelia</i> Species Possessing Glabrous and Pubescent Leaves
resolves10.1093/genetics/147.3.1381
Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes
resolves10.1146/annurev.arplant.043008.092122
Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition
resolves10.1101/gr.081026.108
Many or most genes in <i>Arabidopsis</i> transposed after the origin of the order Brassicales
resolves10.1105/tpc.107.050419
G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in<i>Arabidopsis</i>
resolves10.1101/gr.3681406
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
resolves10.1073/pnas.94.13.6809
DNA sequence evidence for the segmental allotetraploid origin of maize
resolves10.2307/3558427
A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C<sub>4</sub> photosynthesis
resolves10.1126/science.1068275
A Draft Sequence of the Rice Genome (
<i>Oryza sativa</i>
L. ssp.
<i>japonica</i>
)
resolves10.1073/pnas.070430597
Genome organization in dicots: Genome duplication in
<i>Arabidopsis</i>
and synteny between soybean and
<i>Arabidopsis</i>
resolves10.1093/bioinformatics/bth397
DAGchainer: a tool for mining segmental genome duplications and synteny
resolves10.1017/S0016672306008020
Comparative gene mapping in <i>Arabidopsis lyrata</i> chromosomes 1 and 2 and the corresponding <i>A. thaliana</i> chromosome 1: recombination rates, rearrangements and centromere location
resolves10.1042/bj1010103
Photosynthesis by sugar-cane leaves. A new carboxylation reaction and the pathway of sugar formation
resolves10.1534/genetics.104.037051
Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution
resolves10.1038/nature06148
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
resolves10.1101/gr.4064205
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
resolves10.1093/genetics/160.4.1651
Gene Loss, Silencing and Activation in a Newly Synthesized Wheat Allotetraploid
resolves10.1038/ng1063
Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat
resolves10.1534/genetics.106.057182
Centromere Locations and Associated Chromosome Rearrangements in
<i>Arabidopsis lyrata</i>
and
<i>A. thaliana</i>
resolves10.1534/genetics.105.048215
Comprehensive Molecular Cytogenetic Analysis of Sorghum Genome Architecture: Distribution of Euchromatin, Heterochromatin, Genes and Recombination in Comparison to Rice
resolves10.3732/ajb.92.4.761
Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species—<i>Capsella rubella</i>, <i>Arabidopsis lyrata</i> subsp. <i>petraea</i>, and <i>A. thaliana</i>
resolves10.1073/pnas.160271297
Comparing sequenced segments of the tomato and
<i>Arabidopsis</i>
genomes: Large-scale duplication followed by selective gene loss creates a network of synteny
resolves10.1534/genetics.103.022343
Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana
resolves10.1073/pnas.121064698
Protein-coding genes are epigenetically regulated in
<i>Arabidopsis</i>
polyploids
resolves10.1007/s001220100658
Genome organization in dicots. II. Arabidopsis as a ’bridging species’ to resolve genome evolution events among legumes
resolves10.1101/gr.194501
Comparative Genomics Between Rice and
<i>Arabidopsis</i>
Shows Scant Collinearity in Gene Order
resolves10.1071/BT03023
The ecology, phytosociology and stand structure of an ancient endemic plant Lomatia tasmanica (Proteaceae) approaching extinction
resolves10.1093/genetics/154.1.459
The Probability of Duplicate Gene Preservation by Subfunctionalization
resolves10.1111/j.1365-313X.2007.03326.x
How to usefully compare homologous plant genes and chromosomes as DNA sequences
resolves10.1104/pp.108.124867
Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids
resolves10.1101/gr.GR-1617R
Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana
resolves10.1038/nature06856
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
resolves10.1371/journal.pcbi.0020130
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
resolves10.1093/genetics/148.3.929
Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene
resolves10.1105/tpc.13.8.1735
Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops-Triticum) Group
resolves10.1560/E282-PV55-G4XT-DRWJ
Rapid differentiation of homeologous chromosomes in newly-formed allopolyploid wheat
resolves10.1038/nrg1806
Leafing through the genomes of our major crop plants: strategies for capturing unique information
resolves10.1073/pnas.0307901101
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
resolves10.1016/j.tig.2006.09.003
Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
resolves10.1038/ng1296-380
Toward a unified genetic map of higher plants, transcending the monocot–dicot divergence
resolves10.1080/10635150590945359
Placing Paleopolyploidy in Relation to Taxon Divergence: A Phylogenetic Analysis in Legumes Using 39 Gene Families
resolves10.1111/j.1095-8312.2004.00350.x
Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae)
resolves10.1126/science.1139158
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
resolves10.2307/3558329
Phylogenetic analysis of tribe Salsoleae (Chenopodiaceae) based on ribosomal ITS sequences: implications for the evolution of photosynthesis types
resolves10.1111/j.1365-313X.2004.02244.x
Conservation of the microstructure of genome segments in <i>Brassica napus</i> and its diploid relatives
resolves10.1105/tpc.13.4.979
Comparative Sequence Analysis Reveals Extensive Microcolinearity in the <i>Lateral Suppressor</i> Regions of the Tomato, Arabidopsis, and Capsella Genomes
resolves10.1093/nar/30.11.2316
Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project
resolves10.1006/anbo.1998.0746
Evidence that a Recent Increase in Maize Genome Size was Caused by the Massive Amplification of Intergene Retrotransposons
resolves10.1104/pp.84.3.796
Environmental Effects on Photosynthesis, Nitrogen-Use Efficiency, and Metabolite Pools in Leaves of Sun and Shade Plants
resolves10.1016/j.tig.2004.07.008
Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
resolves10.1105/tpc.13.8.1749
Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and Allopolyploidy in Wheat
resolves10.1101/gr.2179004
Building Genomic Profiles for Uncovering Segmental Homology in the Twilight Zone
resolves10.1007/s10142-006-0033-4
Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes
resolves10.1073/pnas.92.17.7719
Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution.
resolves10.1093/bioinformatics/18.1.92
Automated ortholog inference from phylogenetic trees and
calculation of orthology reliability
resolves10.1101/gr1305203
Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database
resolves10.1073/pnas.131568198
Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in
<i>Drosophila</i>
resolves10.1073/pnas.051605998
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals
resolves10.1101/gr.080978.108
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
resolves10.1101/gr.4708406
Following tetraploidy in an <i>Arabidopsis</i> ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
resolves10.1126/science.1128691
The Genome of Black Cottonwood,
<i>Populus trichocarpa</i>
(Torr. & Gray)
resolves10.1101/gr.400202
The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between
<i>Arabidopsis</i>
and Rice
resolves10.1016/S0168-9525(02)02796-8
Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice
resolves10.1016/j.tig.2008.05.005
Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects
resolves10.1186/gb-2009-10-6-r68
Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses
resolves10.1111/j.1469-8137.2004.01293.x
Duplication and DNA segmental loss in the rice genome: implications for diploidization
resolves10.1534/genetics.107.073197
Extensive Concerted Evolution of Rice Paralogs and the Road to Regaining Independence
resolves10.1101/gr.087288.108
Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
resolves10.1186/1471-2105-7-447
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
resolves10.1007/PL00006502
Rates of Nucleotide Substitution in Angiosperm Mitochondrial DNA Sequences and Dates of Divergence Between Brassica and Other Angiosperm Lineages
resolves10.1093/oxfordjournals.molbev.a025957
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
resolves10.1093/genetics/155.1.431
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
resolves10.1126/science.1068037
A Draft Sequence of the Rice Genome (
<i>Oryza sativa</i>
L. ssp.
<i>indica</i>
)
resolves10.1186/1471-2105-3-14
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
The 6 references without a DOI — listed, not checked
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no DOI — not checkedB85
no DOI — not checkedBiology of Plants
no DOI — not checked118. Soltis DE, Soltis PS, Endress PK, Chase MW. 2005. Phylogeny and Evolution of Angiosperms. Sunderland, MA: Sinauer. 336 pp.
no DOI — not checkedB145
no DOI — not checked147. Younghusband F. 1926. The Epic of Mount Everest. London: Arnold. 319 pp.
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