A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selectionw

Roei Sterken, Raphaël Kiekens, Emmy Coppens, Iise Vercauteren, Marc Zabeau, Dirk Lnzé, Jonathan Flowers, Marnik Vuylsteke

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)2987-2998
Number of pages12
JournalPlant Cell
Volume21
Issue number10
DOIs
StatePublished - Oct 1 2009

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Metagenomics
cdc Genes
Arabidopsis
cell cycle
Cyclin-Dependent Kinases
Cell Cycle
genes
cyclin-dependent kinase
Genes
Retinoblastoma Genes
Genetic Selection
Proteins
Mutation
natural selection
Arabidopsis thaliana
proteins
genetic polymorphism
mutation
genomics
loci

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology

Cite this

Sterken, R., Kiekens, R., Coppens, E., Vercauteren, I., Zabeau, M., Lnzé, D., ... Vuylsteke, M. (2009). A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selectionw Plant Cell, 21(10), 2987-2998. https://doi.org/10.1105/tpc.109.067017

A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selectionw . / Sterken, Roei; Kiekens, Raphaël; Coppens, Emmy; Vercauteren, Iise; Zabeau, Marc; Lnzé, Dirk; Flowers, Jonathan; Vuylsteke, Marnik.

In: Plant Cell, Vol. 21, No. 10, 01.10.2009, p. 2987-2998.

Research output: Contribution to journalArticle

Sterken, R, Kiekens, R, Coppens, E, Vercauteren, I, Zabeau, M, Lnzé, D, Flowers, J & Vuylsteke, M 2009, 'A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selectionw ', Plant Cell, vol. 21, no. 10, pp. 2987-2998. https://doi.org/10.1105/tpc.109.067017
Sterken, Roei ; Kiekens, Raphaël ; Coppens, Emmy ; Vercauteren, Iise ; Zabeau, Marc ; Lnzé, Dirk ; Flowers, Jonathan ; Vuylsteke, Marnik. / A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selectionw In: Plant Cell. 2009 ; Vol. 21, No. 10. pp. 2987-2998.
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