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Nucleic Acids Research Advance Access originally published online on March 21, 2009
Nucleic Acids Research 2009 37(10):3189-3201; doi:10.1093/nar/gkp183
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Nucleic Acids Research, 2009, Vol. 37, No. 10 3189-3201
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

Piotr A. Ziolkowski1, Grzegorz Koczyk2, Lukasz Galganski1 and Jan Sadowski1,2,*

1Department of Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan and 2Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland

*To whom correspondence should be addressed. Tel: +48 61 8295963; Fax: +48 61 8295949; Email: jsad{at}amu.edu.pl

Received December 17, 2008. Revised March 4, 2009. Accepted March 5, 2009.

Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidopsis thaliana lines, Columbia (Col) and Landsberg erecta (Ler). Based on the resulting alignments large indels (>100 bp) within these two genomes were analysed. There are ~8500 large indels accounting for the differences between the two genomes. The genetic basis of their origin was distinguished as three main categories: unequal recombination (Urec)-derived, illegitimate recombination (Illrec)-derived and transposable elements (TE)-derived. A detailed study of their distribution and size variation along chromosomes, together with a correlation analyses, allowed us to demonstrate the impact of particular recombination-based mechanisms on the plant genome evolution. The results show that unequal recombination is not efficient in the removal of TEs within the pericentromeric regions. Moreover, we discovered an unexpectedly high influence of large indels on gene evolution pointing out significant differences between the various gene families. For the first time, we present convincing evidence that somatic events do play an important role in plant genome evolution.


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