Structural and functional partitioning of bread wheat chromosome 3B

被引：445

作者：

Choulet, Frederic ^{[1
,2
]}

Alberti, Adriana ^{[3
]}

Theil, Sebastien ^{[1
,2
]}

Glover, Natasha ^{[1
,2
]}

Barbe, Valerie ^{[3
]}

Daron, Josquin ^{[1
,2
]}

Pingault, Lise ^{[1
,2
]}

Sourdille, Pierre ^{[1
,2
]}

Couloux, Arnaud ^{[3
]}

Paux, Etienne ^{[1
,2
]}

Leroy, Philippe ^{[1
,2
]}

Mangenot, Sophie ^{[3
]}

Guilhot, Nicolas ^{[1
,2
]}

Le Gouis, Jacques ^{[1
,2
]}

Balfourier, Francois ^{[1
,2
]}

Alaux, Michael ^{[4
]}

Jamilloux, Veronique ^{[4
]}

Poulain, Julie ^{[3
]}

Durand, Celine ^{[3
]}

Bellec, Arnaud ^{[5
]}

Gaspin, Christine ^{[6
]}

Safar, Jan ^{[7
]}

Dolezel, Jaroslav ^{[7
]}

Rogers, Jane ^{[8
]}

Vandepoele, Klaas ^{[9
,10
]}

Aury, Jean-Marc ^{[3
]}

Mayer, Klaus ^{[11
]}

Berges, Helene ^{[5
]}

Quesneville, Hadi ^{[4
]}

Wincker, Patrick ^{[3
,12
,13
]}

Feuillet, Catherine ^{[1
,2
]}

机构：

[1] INRA, UMR1095, 5 Chemin Beaulieu, F-63039 Clermont Ferrand, France

[2] Univ Blaise Pascal, UMR1095, F-63039 Clermont Ferrand, France

[3] Commissariat Energie Atom & Energies Alternat, Direct Sci Vivant, Inst Genom, F-91000 Evry, France

[4] INRA Versailles, Res Unit Genom Info, UR1164, INRA, F-78026 Versailles, France

[5] INRA, UPR 1258, Ctr Natl Ressources Genom Vegetales, F-31326 Castanet Tolosan, France

[6] INRA, Biometrie & Intelligence Artificielle, F-31326 Castanet Tolosan, France

[7] Inst Expt Bot, Ctr Reg Hana Biotechnol & Agr Res, CZ-78371 Olomouc, Czech Republic

[8] Genome Anal Ctr, Norwich NR4 7UH, Norfolk, England

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

[10] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

[11] Helmholtz Zentrum Muenchen, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, D-85764 Neuherberg, Germany

[12] CNRS, UMR 8030, F-91000 Evry, France

[13] Univ Evry, CP5706 Evry, Evry, France

来源：

SCIENCE | 2014年 / 345卷 / 6194期

基金：

英国生物技术与生命科学研究理事会;

关键词：

TRANSPOSABLE ELEMENTS; GENE DUPLICATION; GENOME SEQUENCE; COMPLEX GENOMES; DRAFT GENOME; EVOLUTION; RECOMBINATION; DIVERSITY; MAP; KARYOTYPE;

D O I：

10.1126/science.1249721

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter-and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.

引用

页数：7

共 56 条

[1] Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates [J].

Akhunov, ED ;

Akhunova, AR ;

Linkiewicz, AM ;

Dubcovsky, J ;

Hummel, D ;

Lazo, G ;

Chao, SM ;

Anderson, OD ;

David, J ;

Qi, LL ;

Echalier, B ;

Gill, BS ;

Gustafson, MJP ;

La Rota, M ;

Sorrells, ME ;

Zhang, DS ;

Nguyen, HT ;

Kalavacharla, V ;

Hossain, K ;

Kianian, SF ;

Peng, JH ;

Lapitan, NLV ;

Wennerlind, EJ ;

Nduati, V ;

Anderson, JA ;

Sidhu, D ;

Gill, KS ;

McGuire, PE ;

Qualset, CO ;

Dvorak, J .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (19) :10836-10841

[2] Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome [J].

Baucom, Regina S. ;

Estill, James C. ;

Chaparro, Cristian ;

Upshaw, Naadira ;

Jogi, Ansuya ;

Deragon, Jean-Marc ;

Westerman, Richard P. ;

SanMiguel, Phillip J. ;

Bennetzen, Jeffrey L. .

PLOS GENETICS, 2009, 5 (11)

[3] Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome [J].

Baucom, Regina S. ;

Estill, James C. ;

Leebens-Mack, Jim ;

Bennetzen, Jeffrey L. .

GENOME RESEARCH, 2009, 19 (02) :243-254

[4] Mapping translocation breakpoints using a wheat microarray [J].

Bhat, Prasanna R. ;

Lukaszewski, Adam ;

Cui, Xinping ;

Xu, Jin ;

Svensson, Jan T. ;

Wanamaker, Steve ;

Waines, J. Giles ;

Close, Timothy J. .

NUCLEIC ACIDS RESEARCH, 2007, 35 (09) :2936-2943

[5] Analysis of the breadwheat genome using whole-genome shotgun sequencing [J].

Brenchley, Rachel ;

Spannagl, Manuel ;

Pfeifer, Matthias ;

Barker, Gary L. A. ;

D'Amore, Rosalinda ;

Allen, Alexandra M. ;

McKenzie, Neil ;

Kramer, Melissa ;

Kerhornou, Arnaud ;

Bolser, Dan ;

Kay, Suzanne ;

Waite, Darren ;

Trick, Martin ;

Bancroft, Ian ;

Gu, Yong ;

Huo, Naxin ;

Luo, Ming-Cheng ;

Sehgal, Sunish ;

Gill, Bikram ;

Kianian, Sharyar ;

Anderson, Olin ;

Kersey, Paul ;

Dvorak, Jan ;

McCombie, W. Richard ;

Hall, Anthony ;

Mayer, Klaus F. X. ;

Edwards, Keith J. ;

Bevan, Michael W. ;

Hall, Neil .

NATURE, 2012, 491 (7426) :705-710

[6] Genome Project Standards in a New Era of Sequencing [J].

Chain, P. S. G. ;

Grafham, D. V. ;

Fulton, R. S. ;

FitzGerald, M. G. ;

Hostetler, J. ;

Muzny, D. ;

Ali, J. ;

Birren, B. ;

Bruce, D. C. ;

Buhay, C. ;

Cole, J. R. ;

Ding, Y. ;

Dugan, S. ;

Field, D. ;

Garrity, G. M. ;

Gibbs, R. ;

Graves, T. ;

Han, C. S. ;

Harrison, S. H. ;

Highlander, S. ;

Hugenholtz, P. ;

Khouri, H. M. ;

Kodira, C. D. ;

Kolker, E. ;

Kyrpides, N. C. ;

Lang, D. ;

Lapidus, A. ;

Malfatti, S. A. ;

Markowitz, V. ;

Metha, T. ;

Nelson, K. E. ;

Parkhill, J. ;

Pitluck, S. ;

Qin, X. ;

Read, T. D. ;

Schmutz, J. ;

Sozhamannan, S. ;

Sterk, P. ;

Strausberg, R. L. ;

Sutton, G. ;

Thomson, N. R. ;

Tiedje, J. M. ;

Weinstock, G. ;

Wollam, A. ;

Detter, J. C. .

SCIENCE, 2009, 326 (5950) :236-237

[7] Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat [J].

Charles, Mathieu ;

Belcram, Harry ;

Just, Jeremy ;

Huneau, Cecile ;

Viollet, Agnes ;

Couloux, Arnaud ;

Segurens, Beatrice ;

Carter, Meredith ;

Huteau, Virginie ;

Coriton, Olivier ;

Appels, Rudi ;

Samain, Sylvie ;

Chalhoub, Boulos .

GENETICS, 2008, 180 (02) :1071-1086

[8]

Chen J., 2012, PARAMETRIC STATISTIC

[9] Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces [J].

Choulet, Frederic ;

Wicker, Thomas ;

Rustenholz, Camille ;

Paux, Etienne ;

Salse, Jerome ;

Leroy, Philippe ;

Schlub, Stephane ;

Le Paslier, Marie-Christine ;

Magdelenat, Ghislaine ;

Gonthier, Catherine ;

Couloux, Arnaud ;

Budak, Hikmet ;

Breen, James ;

Pumphrey, Michael ;

Liu, Sixin ;

Kong, Xiuying ;

Jia, Jizeng ;

Gut, Marta ;

Brunel, Dominique ;

Anderson, James A. ;

Gill, Bikram S. ;

Appels, Rudi ;

Keller, Beat ;

Feuillet, Catherine .

PLANT CELL, 2010, 22 (06) :1686-1701

[10] Genome relationships: The grass model in current research [J].

Devos, KM ;

Gale, MD .

PLANT CELL, 2000, 12 (05) :637-646

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