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

Tina T Hu, Pedro Pattyn UGent, Erica G Bakker, Jun Cao, Jan-Fang Cheng, Richard M Clark, Noah Fahlgren, Jeffrey Fawcett UGent, Jane Grimwood, Heidrun Gundlach, et al. (2011) NATURE GENETICS. 43(5). p.476-481
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
EXPANSION, IDENTIFICATION, ALIGNMENT, PLANTS, TRANSPOSABLE ELEMENTS, DNA LOSS, ANGIOSPERM GENOMES, EUKARYOTIC GENOME, EVOLUTION, THALIANA
journal title
NATURE GENETICS
Nature Genet.
volume
43
issue
5
pages
476 - 481
Web of Science type
Article
Web of Science id
000289972600020
JCR category
GENETICS & HEREDITY
JCR impact factor
35.532 (2011)
JCR rank
2/155 (2011)
JCR quartile
1 (2011)
ISSN
1061-4036
DOI
10.1038/ng.807
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1864409
handle
http://hdl.handle.net/1854/LU-1864409
date created
2011-08-01 17:22:28
date last changed
2016-12-19 15:41:56
@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},
}

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.