Reference health
The potential of genomics in plant systematics
95/95 checkable references clean · checked 2026-07-22
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
4 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 95 checked references that resolve
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Erratum From—Polyploid Evolution in Spartina: Dealing with Highly Redundant Hybrid Genomes
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An SNP map of the human genome generated by reduced representation shotgun sequencing
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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
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Coverage‐based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (<i>Cicer arietinum</i>; Fabaceae), a crop species without a reference genome
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Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
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Characterization of duplicate gene evolution in the recent natural allopolyploid <i>Tragopogon miscellus</i> by next‐generation sequencing and Sequenom iPLEX MassARRAY genotyping
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Transcriptomic Shock Generates Evolutionary Novelty in a Newly Formed, Natural Allopolyploid Plant
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Rapid identification of thousands of copperhead snake (<i>Agkistrodon contortrix</i>) microsatellite loci from modest amounts of 454 shotgun genome sequence
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Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions
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Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation)
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Extensive chromosomal variation in a recently formed natural allopolyploid species,
<i>Tragopogon miscellus</i>
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An assessment of karyotype restructuring in the neoallotetraploid Tragopogon miscellus (Asteraceae)
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Anatomical, biochemical, and photosynthetic responses to recent allopolyploidy in <i>Glycine dolichocarpa</i> (Fabaceae)
resolves10.1093/nar/gkn502
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
resolves10.1038/nrg3012
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
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A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
resolves10.1534/genetics.109.113753
A Fluorescence <i>in Situ</i> Hybridization System for Karyotyping Soybean
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Genomic Changes in Resynthesized
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and Their Effect on Gene Expression and Phenotype
resolves10.1080/17550874.2012.745909
Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics
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Targeted sequence capture as a powerful tool for evolutionary analysis<sup>1</sup>
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Mining <i>Arabidopsis thaliana</i> RNA‐seq data with Integrated Genome Browser reveals stress‐induced alternative splicing of the putative splicing regulator SR45a
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Next‐generation sequencing‐based transcriptomic and proteomic analysis of the common reed, <i>Phragmites australis</i> (Poaceae), reveals genes involved in invasiveness and rhizome specificity
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Development of anonymous cDNA microarrays to study changes to the<i>Senecio</i>floral transcriptome during hybrid speciation
resolves10.1016/j.cub.2006.06.071
Transcriptome Shock after Interspecific Hybridization in Senecio Is Ameliorated by Genome Duplication
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Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in
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resolves10.1111/j.1365-294X.2010.04926.x
Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae)
resolves10.1007/978-3-642-31442-1_13
Allopolyploid Speciation in Action: The Origins and Evolution of Senecio cambrensis
resolves10.1186/1471-2229-10-204
Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing
resolves10.3732/ajb.1100312
A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA‐seq in plant species
resolves10.1038/nature11543
A physical, genetic and functional sequence assembly of the barley genome
resolves10.1073/pnas.0709121104
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
resolves10.1371/journal.pone.0050226
Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes
resolves10.1007/Bf00037014
Analysis of a repetitive DNA family from Arabidopsis arenosa and relationships between Arabidopsis species
resolves10.3732/ajb.1100570
Ultra‐barcoding in cacao (<i>Theobroma</i> spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA
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<i>Aquilegia</i>: A New Model for Plant Development, Ecology, and Evolution
resolves10.3732/ajb.1100340
A comparison of statistical methods for detecting differentially expressed genes from RNA‐seq data
resolves10.1111/j.1469-8137.2010.03187.x
RNAi‐mediated down‐regulation of <i>DCL1</i> and <i>AGO1</i> induces developmental changes in resynthesized <i>Arabidopsis</i> allotetraploids
resolves10.3732/ajb.1100313
Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression
resolves10.1371/journal.pone.0003353
Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)
resolves10.1186/1471-2164-8-427
Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula
resolves10.1371/journal.pone.0027335
Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia
resolves10.1007/s10577-007-1180-8
An interspecific hybrid as a tool to study phylogenetic relationships in plants using the GISH technique
resolves10.1111/j.1469-8137.2009.03139.x
Analysis of gene expression in resynthesized <i>Brassica napus</i> allotetraploids: transcriptional changes do not explain differential protein regulation
resolves10.1002/tax.574014
Putative parentage of six Old World polyploids in
<i>Tragopogon</i>
L. (Asteraceae: Scorzonerinae) based on ITS, ETS, and plastid sequence data
resolves10.1111/j.1469-8137.2009.03141.x
Photoperiod‐dependent floral reversion in the natural allopolyploid <i>Arabidopsis suecica</i>
resolves10.3732/ajb.1100537
Phylogenomic analysis of transcriptome data elucidates co‐occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)
resolves10.1186/1471-2229-6-17
resolves10.1073/pnas.0708072104
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
resolves10.1073/pnas.0907801107
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots
resolves10.3732/ajb.89.6.921
The origin of tobacco's T genome is traced to a particular lineage within <i>Nicotiana tomentosiformis</i> (Solanaceae)
resolves10.1111/j.1469-8137.2009.03164.x
Tandem duplication of the <i>FLC</i> locus and the origin of a new gene in <i>Arabidopsis</i> related species and their functional implications in allopolyploids
resolves10.1016/j.ympev.2012.08.026
Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing
resolves10.1186/1741-7007-7-84
Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes
resolves10.1186/1471-2148-12-100
Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)
resolves10.3417/2007176
A Renaissance of Cytogenetics: Studies in Polyploidy and Chromosomal Evolution<sup>1</sup>
resolves10.1371/journal.pone.0036963
Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum
resolves10.1007/978-3-642-31442-1_8
Maize (Zea Mays) as a Model for Studying the Impact of Gene and Regulatory Sequence Loss Following Whole-Genome Duplication
resolves10.1126/science.1163197
Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
resolves10.3732/ajb.1000481
Understanding angiosperm diversification using small and large phylogenetic trees
resolves10.1007/978-3-642-31442-1_14
The Early Stages of Polyploidy: Rapid and Repeated Evolution in Tragopogon
resolves10.3732/ajb.1100491
Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae
resolves10.3732/ajb.1100335
Navigating the tip of the genomic iceberg: Next‐generation sequencing for plant systematics
resolves10.3732/ajb.1100292
Designing a transcriptome next‐generation sequencing project for a nonmodel plant species<sup>1</sup>
resolves10.3732/apps.1200497
A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes
resolves10.1186/1471-2164-8-132
Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey
resolves10.1007/s10577-009-9077-3
Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology
resolves10.3732/ajb.0800299
Synthetic polyploids of <i>Tragopogon miscellus</i> and <i>T. mirus</i> (Asteraceae): 60 Years after Ownbey's discovery
resolves10.1534/genetics.105.051466
Chromosome-Level Homeology in Paleopolyploid Soybean (<i>Glycine max</i>) Revealed Through Integration of Genetic and Chromosome Maps
resolves10.1007/978-3-642-31442-1_10
Jeans, Genes, and Genomes: Cotton as a Model for Studying Polyploidy
resolves10.1073/pnas.0806446105
Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change
resolves10.1073/pnas.1014138108
Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid
<i>Brassica napus</i>
resolves10.3732/ajb.1100333
Genome‐wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics
resolves10.3732/ajb.1100394
Using next‐generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
The 4 references without a DOI — listed, not checked
no DOI — not checkedAmborella Genome Project. In press. TheAmborellagenome and the evolution of flowering plants. Science
no DOI — not checkedBaird N.A. Etter P.D. Atwood T.S. Currey M.C. Shiver A.L.
no DOI — not checkedRuhfel B.R. Gitzendanner M.A. Soltis P.S. Soltis D.E.&Burleigh J.G.In press. From algae to angiosperms - Inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes.B. M. C. Evol. Biol.
no DOI — not checkedPlant taxonomy: The systematic evaluation of comparative data
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