The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
Open accessAbstract
Significance: One of the most important technological advances by humans is the domestication of plant species for the production of food. We have used high-throughput sequencing to identify changes in DNA sequence and gene expression that differentiate cultivated tomato and its wild relatives. We also identify hundreds of candidate genes that have evolved new protein sequences or have changed expression levels in response to natural selection in wild tomato relatives. Taken together, our analyses provide a snapshot of genome evolution under artificial and natural conditions.
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Cites
R: A Language and Environment for Statistical Computing
R Core Team (2025) · doi:10.32614/r.manuals · Cited by 352,181
The tomato genome sequence provides insights into fleshy fruit evolution
The Tomato Genome Consortium (2012) · Nature · doi:10.1038/nature11119 · Cited by 3,289
Pectin structure and biosynthesis
MOHNEN, D. (2008) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2008.03.006 · Cited by 2,447
Gas chromatography mass spectrometry–based metabolite profiling in plants
Lisec, J., Schauer, N., Kopka, J., Willmitzer, L., & Fernie, A. R. (2006) · Nature Protocols · doi:10.1038/nprot.2006.59 · Cited by 2,170
Self-citationEvo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
Carroll, S. B. (2008) · Cell · doi:10.1016/j.cell.2008.06.030 · Cited by 2,067
Genome sequence and analysis of the tuber crop potato
The Potato Genome Sequencing Consortium (2011) · Nature · doi:10.1038/nature10158 · Cited by 2,065
The Molecular Genetics of Crop Domestication
Doebley, J. F., Gaut, B. S., & Smith, B. D. (2006) · Cell · doi:10.1016/j.cell.2006.12.006 · Cited by 1,979
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
The variation of animals and plants under domestication /
Darwin, C. (1905) · J. Murray eBooks · doi:10.5962/bhl.title.84435 · Cited by 1,707
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I., Lapp, H., et al. (2002) · Genome Research · doi:10.1101/gr.361602 · Cited by 1,654
Cited by
Genomics of crop wild relatives: expanding the gene pool for crop improvement
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De Novo Domestication: An Alternative Route toward New Crops for the Future
Fernie, A. R., & Yan, J. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.03.016 · Cited by 398
Self-citationRon, M., Kajala, K., Pauluzzi, G., Wang, D., Reynoso, M. A., Zumstein, K., Garcha, J., Winte, S., Masson, H., Inagaki, S., et al. (2014) · PLANT PHYSIOLOGY · doi:10.1104/pp.114.239392 · Cited by 389
Self-citationExploring the Diversity of Plant Metabolism
Fang, C., Fernie, A. R., & Luo, J. (2019) · Trends in Plant Science · doi:10.1016/j.tplants.2018.09.006 · Cited by 334
Self-citationPrehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416991111 · Cited by 324
Metadata
- Authors
- Koenig, D., Jiménez-Gómez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., Kumar, R., Covington, M. F., Devisetty, U. K., Tat, A. V., Tohge, T., Bolger, A., Schneeberger, K., Ossowski, S., Lanz, C., Xiong, G., Taylor-Teeples, M., Brady, S. M., Pauly, M., Weigel, D., Usadel, B., Fernie, A. R., Peng, J., Sinha, N. R., & Maloof, J. N.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2013-06-26
- Volume
- 110
- Issue
- 28
- Pages
- E2655-62
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2016017635
- Cited by
- 368
- References
- 66
- FWCI
- 22.86
- Type
- journal article
- Language
- en
- Open access
- green
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- Koenig, D., Jiménez-Gómez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., Kumar, R., Covington, M. F., Devisetty, U. K., Tat, A. V., Tohge, T., Bolger, A., Schneeberger, K., Ossowski, S., Lanz, C., Xiong, G., Taylor-Teeples, M., Brady, S. M., Pauly, M., . . . Maloof, J. N. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1309606110
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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