A Population Genomics Study of the Arabidopsis Core Cell Cycle Genes Shows the Signature of Natural Selection |
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| Authors: | Roel Sterken Rapha?l Kiekens Emmy Coppens Ilse Vercauteren Marc Zabeau Dirk Inzé Jonathan Flowers Marnik Vuylsteke |
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| Affiliation: | aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium;bDepartment of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium;cDepartment of Biology, New York University, New York, New York 10003;dCenter for Genomics and Systems Biology, New York University, New York, New York 10003 |
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| Abstract: | Large-scale comparison of sequence polymorphism and divergence at numerous genomic loci within and between closely related species can reveal signatures of natural selection. Here, we present a population genomics study based on direct sequencing of 61 mitotic cell cycle genes from 30 Arabidopsis thaliana accessions and comparison of the resulting data to the close relative Arabidopsis lyrata. We found that the Arabidopsis core cell cycle (CCC) machinery is not highly constrained but is subject to different modes of selection. We found patterns of purifying selection for the cyclin-dependent kinase (CDK), CDK subunit, retinoblastoma, and WEE1 gene families. Other CCC gene families often showed a mix of one or two constrained genes and relaxed purifying selection on the other genes. We found several large effect mutations in CDKB1;2 that segregate in the species. We found a strong signature of adaptive protein evolution in the Kip-related protein KRP6 and departures from equilibrium at CDKD;1 and CYCA3;3 consistent with the operation of selection in these gene regions. Our data suggest that within Arabidopsis, the genetic robustness of cell cycle–related processes is more due to functional redundancy than high selective constraint. |
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