The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
Open accessAbstract
Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5–12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Role of duplicate genes in genetic robustness against null mutations
Gu, Z., Steinmetz, L. M., Gu, X., Scharfe, C., Davis, R. W., & Li, W.-H. (2003) · Nature · doi:10.1038/nature01198 · Cited by 889
Genetic interactions reveal the evolutionary trajectories of duplicate genes
VanderSluis, B., Bellay, J., Musso, G., Costanzo, M., Papp, B., Vizeacoumar, F. J., Baryshnikova, A., Andrews, B., Boone, C., & Myers, C. L. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.82 · Cited by 110
Cited by
Improved maize reference genome with single-molecule technologies
Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C.-S., et al. (2017) · Nature · doi:10.1038/nature22971 · Cited by 1,210
Self-citationGenome evolution in the allotetraploid frog Xenopus laevis
Session, A. M., Uno, Y., Kwon, T., Chapman, J. A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., et al. (2016) · Nature · doi:10.1038/nature19840 · Cited by 949
Albalat, R., & Cañestro, C. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.39 · Cited by 775
Polyploidy and genome evolution in plants
Soltis, P. S., Marchant, D. B., Van de Peer, Y., & Soltis, D. E. (2015) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.11.003 · Cited by 773
Freeling, M., Woodhouse, M. R., Subramaniam, S., Turco, G., Lisch, D., & Schnable, J. C. (2012) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2012.01.015 · Cited by 198
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Metadata
- Authors
- Schnable, J. C., Springer, N. M., & Freeling, M.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2011-02-22
- Volume
- 108
- Issue
- 10
- Pages
- 4069-4074
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2076658876
- Cited by
- 708
- References
- 4
- FWCI
- 47.95
- Type
- journal article
- Language
- en
- Open access
- green
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