The Capsella rubella genome and the genomic consequences of rapid mating system evolution

被引：289

作者：

Slotte, Tanja ^{[1
,2
,3
]}

Hazzouri, Khaled M. ^{[1
,4
]}

Agren, J. Arvid ^{[1
]}

Koenig, Daniel ^{[5
]}

Maumus, Florian ^{[6
]}

Guo, Ya-Long ^{[7
]}

Steige, Kim ^{[2
]}

Platts, Adrian E. ^{[8
]}

Escobar, Juan S. ^{[1
]}

Newman, L. Killian ^{[1
]}

Wang, Wei ^{[1
]}

Mandakova, Terezie ^{[9
]}

Vello, Emilio ^{[8
]}

Smith, Lisa M. ^{[5
]}

Henz, Stefan R. ^{[5
]}

Steffen, Joshua ^{[10
,11
]}

Takuno, Shohei ^{[12
,13
]}

Brandvain, Yaniv ^{[14
]}

Coop, Graham ^{[14
]}

Andolfatto, Peter ^{[15
,16
]}

Hu, Tina T. ^{[15
,16
]}

Blanchette, Mathieu ^{[17
]}

Clark, Richard M. ^{[10
]}

Quesneville, Hadi ^{[6
]}

Nordborg, Magnus ^{[18
]}

Gaut, Brandon S. ^{[12
]}

Lysak, Martin A. ^{[9
]}

Jenkins, Jerry ^{[19
]}

Grimwood, Jane ^{[19
]}

Chapman, Jarrod ^{[20
]}

Prochnik, Simon ^{[20
]}

Shu, Shengqiang ^{[20
]}

Rokhsar, Daniel ^{[20
,21
]}

Schmutz, Jeremy ^{[19
,20
]}

Weigel, Detlef ^{[5
]}

Wright, Stephen I. ^{[1
,22
]}

机构：

[1] Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON, Canada

[2] Uppsala Univ, Dept Evolutionary Biol, Evolutionary Biol Ctr, Uppsala, Sweden

[3] Uppsala Univ, Sci Life Lab, Uppsala, Sweden

[4] New York Univ Abu Dhabi, Ctr Genom & Syst Biol, Abu Dhabi, U Arab Emirates

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

[6] INRA, Ctr Versailles Grignon, Unite Rech Genom Info, F-78026 Versailles, France

[7] Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China

[8] McGill Univ, Dept Biol, Montreal, PQ H3A 1B1, Canada

[9] Masaryk Univ, Lab Plant Cytogen, Cent European Inst Technol CEITEC, Brno, Czech Republic

[10] Univ Utah, Dept Biol, Salt Lake City, UT 84112 USA

[11] Colby Sawyer Coll, Dept Nat Sci, New London, NH USA

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

[13] Univ Calif Davis, Dept Plant Sci, Davis, CA 95616 USA

[14] Univ Calif Davis, Dept Ecol & Evolut, Davis, CA 95616 USA

[15] Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA

[16] Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA

[17] McGill Univ, Sch Comp Sci, Montreal, PQ, Canada

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

[19] HudsonAlpha Inst Biotechnol, Huntsville, AL USA

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

[21] Univ Calif Berkeley, Ctr Integrat Genom, Berkeley, CA 94720 USA

[22] Univ Toronto, Ctr Anal Genome Evolut & Funct, Toronto, ON, Canada

来源：

NATURE GENETICS | 2013年 / 45卷 / 07期

基金：

加拿大自然科学与工程研究理事会; 瑞典研究理事会; 美国国家科学基金会;

关键词：

ARABIDOPSIS-THALIANA; MOLECULAR EVOLUTION; RECENT SPECIATION; SEQUENCE; EXPRESSION; GENES; GRANDIFLORA; ANNOTATION; MUTATIONS; SOFTWARE;

D O I：

10.1038/ng.2669

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The shift from outcrossing to selfing is common in flowering plants(1,2), but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.

引用

页码：831 / U165

页数：7

共 40 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL
ALTSCHUL, SF
GISH, W
MILLER, W
MYERS, EW
LIPMAN, DJ
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
[2] The evolution of plant sexual diversity
Barrett, SCH
[J]. NATURE REVIEWS GENETICS, 2002, 3 (04) : 274 - 284
[3] CHARLESWORTH B, 1986, GENETICS, V112, P359
[4] Breeding systems and genome evolution
Charlesworth, D
Wright, SI
[J]. CURRENT OPINION IN GENETICS & DEVELOPMENT, 2001, 11 (06) : 685 - 690
[5] FUNDAMENTAL CONCEPTS IN GENETICS The genetics of inbreeding depression
Charlesworth, Deborah
Willis, John H.
[J]. NATURE REVIEWS GENETICS, 2009, 10 (11) : 783 - 796
[6] MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, RC
[J]. BMC BIOINFORMATICS, 2004, 5 (1) : 1 - 19
[7] LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
Ellinghaus, David
Kurtz, Stefan
Willhoeft, Ute
[J]. BMC BIOINFORMATICS, 2008, 9 (1)
[8] AN INTEGRATIVE TEST OF THE DEAD-END HYPOTHESIS OF SELFING EVOLUTION IN TRITICEAE (POACEAE)
Escobar, Juan S.
Cenci, Alberto
Bolognini, Jeremy
Haudry, Annabelle
Laurent, Stefan
David, Jacques
Glemin, Sylvain
[J]. EVOLUTION, 2010, 64 (10) : 2855 - 2872
[9] Considering Transposable Element Diversification in De Novo Annotation Approaches
Flutre, Timothee
Duprat, Elodie
Feuillet, Catherine
Quesneville, Hadi
[J]. PLOS ONE, 2011, 6 (01):
[10] Recent speciation associated with the evolution of selfing in Capsella
Foxe, John Paul
Slotte, Tanja
Stahl, Eli A.
Neuffer, Barbara
Hurka, Herbert
Wright, Stephen I.
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (13) : 5241 - 5245

← 1 2 3 4 →