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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

2011; Nature Portfolio; Volume: 43; Issue: 5 Linguagem: Inglês

10.1038/ng.807

1546-1718

Tina T. Hu, Pedro Pattyn, Erica Bakker, Jun Cao, Jan‐Fang Cheng, Richard M. Clark, Noah Fahlgren, Jeffrey A. Fawcett, Jane Grimwood, Heidrun Gundlach, Georg Haberer, Jesse D. Hollister, Stephan Ossowski, Robert P Ottilar, Asaf Salamov, Korbinian Schneeberger, M. Spannagl, Xi Wang, Liang Yang, Mikhail E. Nasrallah, Joy Bergelson, James C. Carrington, Brandon S. Gaut, Jeremy Schmutz, Klaus Mayer, Yves Van de Peer, Igor V. Grigoriev, Magnus Nordborg, Detlef Weigel, Ya‐Long Guo,

Genomics and Phylogenetic Studies

Detlef Weigel and colleagues report the genome sequence of Arabidopsis lyrata. In comparison with the much smaller genome of A. thaliana, from which A. lyrata diverged about 10 million years ago, they find that the reduction in genome size is attributed to a large number of deletions across the genome. We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3× dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis.