Cited by 153Genetic Mapping and Diversity in Plants and AnimalsPlant Molecular Biology ResearchGenomics and Phylogenetic Studies

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The Arabidopsis genome: A foundation for plant research

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Bevan, Michael, Walsh, Sean·2005·Genome Research

DOI 10.1101/gr.3723405

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Abstract

The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana (Arabidopsis). This review summarizes progress made in the past five years and speculates about future developments in Arabidopsis research and its implications for crop science. The provision of large populations of gene disruption lines to the research community has greatly accelerated the impact of genomics on many areas of plant science. The tools and community organization required for plant integrative and systems biology approaches are now ready to accomplish the next big step in plant biology—the integration of knowledge and modeling of biological processes. In the future, plant science will continue to be enriched by the alignment of high-quality basic research (generally conducted in Arabidopsis), with strategic objectives in crop plants. The sequence and analysis of an increasing number of crop plant genomes enhance this alignment and provide new insights into genome evolution and crop plant domestication.

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Baginsky, S., & Gruissem, W. (2004) · Journal of Experimental Botany · doi:10.1093/jxb/erh104 · Cited by 87
Beyond the Arabidopsis Genome: Opportunities for Comparative Genomics
Hall, A. E., Fiebig, A., & Preuss, D. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.004051 · Cited by 87
Haplotype Structure and Phenotypic Associations in the Chromosomal Regions Surrounding Two Arabidopsis thaliana Flowering Time LociSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY781906, AY785055.
Hagenblad, J., Tang, C., Molitor, J., Werner, J. D., Zhao, K., Zheng, H., Marjoram, P., Weigel, D., & Nordborg, M. (2004) · Genetics · doi:10.1534/genetics.104.029470 · Cited by 69
AMPDB: the Arabidopsis Mitochondrial Protein Database
Heazlewood, J. L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki048 · Cited by 67
Epigenomic mapping in Arabidopsis using tiling microarrays
Martienssen, R. A., Doerge, R. W., & Colot, V. (2005) · Chromosome Research · doi:10.1007/s10577-005-1507-2 · Cited by 52
Which gene did you mean?
Mons, B. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-142 · Cited by 45
Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,
Xiao, Y., Malik, M., Whitelaw, C. A., & Town, C. D. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.010207 · Cited by 29
Orphan transcripts in Arabidopsis thaliana : identification of several hundred previously unrecognized genes
Riaño‐Pachón, D. M., Drèyer, I., & Mueller‐Roeber, B. (2005) · The Plant Journal · doi:10.1111/j.1365-313x.2005.02438.x · Cited by 19

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1 of the 99 references couldn’t be matched to a known paper.

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Plant responses to plant growth-promoting rhizobacteria
van Loon, L. C. (2007) · European Journal of Plant Pathology · doi:10.1007/s10658-007-9165-1 · Cited by 915
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)
Wang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., Huang, L., Chen, X., & Li, Y. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-726 · Cited by 433
Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
Parchman, T. L., Geist, K. S., Grahnen, J. A., Benkman, C. W., & Buerkle, C. A. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-180 · Cited by 446
Alternative oxidases in Arabidopsis: A comparative analysis of differential expression in the gene family provides new insights into function of non-phosphorylating bypasses
Clifton, R., Millar, A. H., & Whelan, J. (2006) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2006.03.009 · Cited by 346
A Phenome-Based Functional Analysis of Transcription Factors in the Cereal Head Blight Fungus, Fusarium graminearum
Son, H., Seo, Y., Min, K., Park, A. R., Lee, J., Jin, J., Lin, Y., Cao, P., Hong, S.-Y., Kim, E., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002310 · Cited by 330

See all 153

Authors: Bevan, M., & Walsh, S.
Affiliations: John Innes Centre (GB)
Corresponding author: Bevan, Michael
ORCID: Bevan, Michael
Walsh, Sean
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2005-12
Volume: 15
Issue: 12
Pages: 1632-1642
ISSN: 1088-9051 (ISSN-L)
DOI: 10.1101/gr.3723405
OpenAlex: W2166592994
Cited by: 153
References: 99
Citations by year: 2026: 4 · 2025: 3 · 2024: 5 · 2023: 4 · 2022: 8 · 2021: 2 · 2020: 15 · 2019: 10 · 2018: 5 · 2017: 8 · 2016: 6 · 2015: 5 · 2014: 7 · 2013: 7 · 2012: 9
Type: posted content
Language: en
Open access: hybrid
doi.org
Licence: other-oa
Locations: Genome Research (publishedVersion, other-oa)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: Arabidopsis thaliana, plant genome, gene function discovery, plant systems biology, mathematical biology, cultivated plants, genome evolution, crop domestication, plant genomics
MeSH terms: Arabidopsis, Sequence Analysis, DNA, Gene Expression Regulation, Plant, DNA, Plant, Genome, Plant, Genomics

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The Arabidopsis genome: A foundation for plant research

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