Advanced search
1 file | 1.18 MB

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

(2011) NATURE GENETICS. 43(5). p.476-481
Author
Organization
Project
Bioinformatics: from nucleotids to networks (N2N)
Abstract
We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3x 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.
Keywords
EXPANSION, IDENTIFICATION, ALIGNMENT, PLANTS, TRANSPOSABLE ELEMENTS, DNA LOSS, ANGIOSPERM GENOMES, EUKARYOTIC GENOME, EVOLUTION, THALIANA

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 1.18 MB

Citation

Please use this url to cite or link to this publication:

Chicago
Hu, Tina T, Pedro Pattyn, Erica G Bakker, Jun Cao, Jan-Fang Cheng, Richard M Clark, Noah Fahlgren, et al. 2011. “The Arabidopsis Lyrata Genome Sequence and the Basis of Rapid Genome Size Change.” Nature Genetics 43 (5): 476–481.
APA
Hu, T. T., Pattyn, P., Bakker, E. G., Cao, J., Cheng, J.-F., Clark, R. M., Fahlgren, N., et al. (2011). The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. NATURE GENETICS, 43(5), 476–481.
Vancouver
1.
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J-F, Clark RM, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. NATURE GENETICS. 2011;43(5):476–81.
MLA
Hu, Tina T, Pedro Pattyn, Erica G Bakker, et al. “The Arabidopsis Lyrata Genome Sequence and the Basis of Rapid Genome Size Change.” NATURE GENETICS 43.5 (2011): 476–481. Print.
@article{1864409,
  abstract     = {We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3x 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.},
  author       = {Hu, Tina T and Pattyn, Pedro and Bakker, Erica G and Cao, Jun and Cheng, Jan-Fang and Clark, Richard M and Fahlgren, Noah and Fawcett, Jeffrey and Grimwood, Jane and Gundlach, Heidrun and Haberer, Georg and Hollister, Jesse D and Ossowski, Stephan and Ottilar, Robert P and Salamov, Asaf A and Schneeberger, Korbinian and Spannagl, Manuel and Wang, Xi and Yang, Liang and Nasrallah, Mikhail E and Bergelson, Joy and Carrington, James C and Gaut, Brandon S and Schmutz, Jeremy and Mayer, Klaus FX and Van de Peer, Yves and Grigoriev, Igor V and Nordborg, Magnus and Weigel, Detlef and Guo, Ya-Long},
  issn         = {1061-4036},
  journal      = {NATURE GENETICS},
  keyword      = {EXPANSION,IDENTIFICATION,ALIGNMENT,PLANTS,TRANSPOSABLE ELEMENTS,DNA LOSS,ANGIOSPERM GENOMES,EUKARYOTIC GENOME,EVOLUTION,THALIANA},
  language     = {eng},
  number       = {5},
  pages        = {476--481},
  title        = {The Arabidopsis lyrata genome sequence and the basis of rapid genome size change},
  url          = {http://dx.doi.org/10.1038/ng.807},
  volume       = {43},
  year         = {2011},
}

Altmetric
View in Altmetric
Web of Science
Times cited: