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

Tina T. Hu; Pedro Pattyn; Erica G. 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 A. Salamov; Korbinian Schneeberger; Manuel Spannagl; Xi Wang; Liang Yang; Mikhail E. Nasrallah; Joy Bergelson; James C. Carrington; Brandon S. Gaut; Jeremy Schmutz; Klaus F.X. Mayer; Yves Van De Peer; Igor V. Grigoriev; Magnus Nordborg; Detlef Weigel; Ya Long Guo

doi:10.1038/ng.807

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

Tina T. Hu, Pedro Pattyn, Erica G. 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 A. Salamov, Korbinian Schneeberger, Manuel Spannagl, Xi Wang, Liang Yang, Mikhail E. NasrallahJoy Bergelson, James C. Carrington, Brandon S. Gaut, Jeremy Schmutz, Klaus F.X. Mayer, Yves Van De Peer, Igor V. Grigoriev, Magnus Nordborg, Detlef Weigel, Ya Long Guo

Biology and Genomics

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Pages (from-to)	476-483
Number of pages	8
Journal	Nature Genetics
Volume	43
Issue number	5
DOIs	https://doi.org/10.1038/ng.807
State	Published - May 2011

ASJC Scopus subject areas

Genetics

Access to Document

10.1038/ng.807

Cite this

Hu, T. T., Pattyn, P., Bakker, E. G., Cao, J., Cheng, J. F., Clark, R. M., Fahlgren, N., Fawcett, J. A., Grimwood, J., Gundlach, H., Haberer, G., Hollister, J. D., Ossowski, S., Ottilar, R. P., Salamov, A. A., Schneeberger, K., Spannagl, M., Wang, X., Yang, L., ... Guo, Y. L. (2011). The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics, 43(5), 476-483. https://doi.org/10.1038/ng.807

Hu, TT, Pattyn, P, Bakker, EG, Cao, J, Cheng, JF, Clark, RM, Fahlgren, N, Fawcett, JA, Grimwood, J, Gundlach, H, Haberer, G, Hollister, JD, Ossowski, S, Ottilar, RP, Salamov, AA, Schneeberger, K, Spannagl, M, Wang, X, Yang, L, Nasrallah, ME, Bergelson, J, Carrington, JC, Gaut, BS, Schmutz, J, Mayer, KFX, Van De Peer, Y, Grigoriev, IV, Nordborg, M, Weigel, D & Guo, YL 2011, 'The Arabidopsis lyrata genome sequence and the basis of rapid genome size change', Nature Genetics, vol. 43, no. 5, pp. 476-483. https://doi.org/10.1038/ng.807

@article{00e03e85574640b29e8ec6f12f96d6c9,

title = "The Arabidopsis lyrata genome sequence and the basis of rapid genome size change",

abstract = "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.",

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

year = "2011",

month = may,

doi = "10.1038/ng.807",

language = "English (US)",

volume = "43",

pages = "476--483",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "5",

}

TY - JOUR

T1 - The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

AU - Hu, Tina T.

AU - Pattyn, Pedro

AU - Bakker, Erica G.

AU - Cao, Jun

AU - Cheng, Jan Fang

AU - Clark, Richard M.

AU - Fahlgren, Noah

AU - Fawcett, Jeffrey A.

AU - Grimwood, Jane

AU - Gundlach, Heidrun

AU - Haberer, Georg

AU - Hollister, Jesse D.

AU - Ossowski, Stephan

AU - Ottilar, Robert P.

AU - Salamov, Asaf A.

AU - Schneeberger, Korbinian

AU - Spannagl, Manuel

AU - Wang, Xi

AU - Yang, Liang

AU - Nasrallah, Mikhail E.

AU - Bergelson, Joy

AU - Carrington, James C.

AU - Gaut, Brandon S.

AU - Schmutz, Jeremy

AU - Mayer, Klaus F.X.

AU - Van De Peer, Yves

AU - Grigoriev, Igor V.

AU - Nordborg, Magnus

AU - Weigel, Detlef

AU - Guo, Ya Long

PY - 2011/5

Y1 - 2011/5

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=79955468851&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79955468851&partnerID=8YFLogxK

U2 - 10.1038/ng.807

DO - 10.1038/ng.807

M3 - Article

C2 - 21478890

AN - SCOPUS:79955468851

SN - 1061-4036

VL - 43

SP - 476

EP - 483

JO - Nature Genetics

JF - Nature Genetics

IS - 5

ER -

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

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this