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

被引：644

作者：

Hu, Tina T. ^{[2
]}

Pattyn, Pedro ^{[3
,4
]}

Bakker, Erica G. ^{[5
,6
,7
]}

Cao, Jun ^{[1
]}

Cheng, Jan-Fang ^{[8
]}

Clark, Richard M. ^{[1
]}

Fahlgren, Noah ^{[6
,9
]}

Fawcett, Jeffrey A. ^{[3
,4
]}

Grimwood, Jane ^{[8
,10
]}

Gundlach, Heidrun ^{[11
]}

Haberer, Georg ^{[11
]}

Hollister, Jesse D. ^{[12
]}

Ossowski, Stephan

Ottilar, Robert P. ^{[8
]}

Salamov, Asaf A. ^{[8
]}

Schneeberger, Korbinian ^{[1
]}

Spannagl, Manuel ^{[11
]}

Wang, Xi ^{[11
]}

Yang, Liang ^{[12
]}

Nasrallah, Mikhail E. ^{[13
]}

Bergelson, Joy ^{[5
]}

Carrington, James C. ^{[6
,9
]}

Gaut, Brandon S. ^{[12
]}

Schmutz, Jeremy ^{[8
,10
]}

Mayer, Klaus F. X. ^{[11
]}

Van de Peer, Yves ^{[3
,4
]}

Grigoriev, Igor V. ^{[8
]}

Nordborg, Magnus ^{[2
,14
]}

Weigel, Detlef ^{[1
]}

Guo, Ya-Long ^{[1
]}

机构：

[1] Max Planck Inst Dev Biol, Dept Mol Biol, Tubingen, Germany

[2] Univ So Calif, Los Angeles, CA USA

[3] Univ Ghent VIB, Dept Plant Syst Biol, B-9052 Ghent, Belgium

[4] Univ Ghent, Dept Plant Biotechnol & Genet, B-9000 Ghent, Belgium

[5] Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA

[6] Oregon State Univ, Ctr Genome Res & Biocomp, Corvallis, OR 97331 USA

[7] Oregon State Univ, Dept Hort, Corvallis, OR 97331 USA

[8] US DOE, Joint Genome Inst, Walnut Creek, CA USA

[9] Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA

[10] Hudson Alpha Inst Biotechnol, Hudson Alpha Genome Sequencing Ctr, Huntsville, AL USA

[11] Helmholtz Ctr Munich, Munich Informat Ctr Prot Sequences, Inst Bioinformat & Syst Biol, Neuherberg, Germany

[12] Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92717 USA

[13] Cornell Univ, Dept Plant Biol, Ithaca, NY USA

[14] Austrian Acad Sci, Gregor Mendel Inst, A-1010 Vienna, Austria

来源：

NATURE GENETICS | 2011年 / 43卷 / 05期

基金：

美国国家科学基金会;

关键词：

TRANSPOSABLE ELEMENTS; DNA LOSS; EVOLUTION; ALIGNMENT; IDENTIFICATION; EXPANSION; THALIANA; SEARCH; PLANTS; RECOMBINATION;

D O I：

10.1038/ng.807

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：476 / +

页数：8

共 65 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[3] Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana [J].

Beilstein, Mark A. ;

Nagalingum, Nathalie S. ;

Clements, Mark D. ;

Manchester, Steven R. ;

Mathews, Sarah .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (43) :18724-18728

[4] Mechanisms of recent genome size variation in flowering plants [J].

Bennetzen, JL ;

Ma, JX ;

Devos, K .

ANNALS OF BOTANY, 2005, 95 (01) :127-132

[5] Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata [J].

Berr, Alexandre ;

Pecinka, Ales ;

Meister, Armin ;

Kreth, Gregor ;

Fuchs, Joerg ;

Blattner, Frank R. ;

Lysak, Martin A. ;

Schubert, Ingo .

PLANT JOURNAL, 2006, 48 (05) :771-783

[6] Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana [J].

Borevitz, Justin O. ;

Hazen, Samuel P. ;

Michael, Todd P. ;

Morris, Geoffrey P. ;

Baxter, Ivan R. ;

Hu, Tina T. ;

Chen, Huaming ;

Werner, Jonathan D. ;

Nordborg, Magnus ;

Salf, David E. ;

Kay, Steve A. ;

Chory, Joanne ;

Weigel, Detlef ;

Jones, Jonathan D. G. ;

Ecker, Joseph R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (29) :12057-12062

[7] Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain [J].

Braumann, Ilka ;

van den Berg, Marco A. ;

Kempken, Frank .

MOLECULAR GENETICS AND GENOMICS, 2008, 280 (04) :319-325

[8] EVOLUTIONARY RATES IN PARTIALLY SELF-FERTILIZING SPECIES [J].

CHARLESWORTH, B .

AMERICAN NATURALIST, 1992, 140 (01) :126-148

[9] Evolution of genes and genomes on the Drosophila phylogeny [J].

Clark, Andrew G. ;

Eisen, Michael B. ;

Smith, Douglas R. ;

Bergman, Casey M. ;

Oliver, Brian ;

Markow, Therese A. ;

Kaufman, Thomas C. ;

Kellis, Manolis ;

Gelbart, William ;

Iyer, Venky N. ;

Pollard, Daniel A. ;

Sackton, Timothy B. ;

Larracuente, Amanda M. ;

Singh, Nadia D. ;

Abad, Jose P. ;

Abt, Dawn N. ;

Adryan, Boris ;

Aguade, Montserrat ;

Akashi, Hiroshi ;

Anderson, Wyatt W. ;

Aquadro, Charles F. ;

Ardell, David H. ;

Arguello, Roman ;

Artieri, Carlo G. ;

Barbash, Daniel A. ;

Barker, Daniel ;

Barsanti, Paolo ;

Batterham, Phil ;

Batzoglou, Serafim ;

Begun, Dave ;

Bhutkar, Arjun ;

Blanco, Enrico ;

Bosak, Stephanie A. ;

Bradley, Robert K. ;

Brand, Adrianne D. ;

Brent, Michael R. ;

Brooks, Angela N. ;

Brown, Randall H. ;

Butlin, Roger K. ;

Caggese, Corrado ;

Calvi, Brian R. ;

de Carvalho, A. Bernardo ;

Caspi, Anat ;

Castrezana, Sergio ;

Celniker, Susan E. ;

Chang, Jean L. ;

Chapple, Charles ;

Chatterji, Sourav ;

Chinwalla, Asif ;

Civetta, Alberto .

NATURE, 2007, 450 (7167) :203-218

[10] Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana [J].

Clark, Richard M. ;

Schweikert, Gabriele ;

Toomajian, Christopher ;

Ossowski, Stephan ;

Zeller, Georg ;

Shinn, Paul ;

Warthmann, Norman ;

Hu, Tina T. ;

Fu, Glenn ;

Hinds, David A. ;

Chen, Huaming ;

Frazer, Kelly A. ;

Huson, Daniel H. ;

Schoelkopf, Bernhard ;

Nordborg, Magnus ;

Raetsch, Gunnar ;

Ecker, Joseph R. ;

Weigel, Detlef .

SCIENCE, 2007, 317 (5836) :338-342

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