Crop genome sequencing: lessons and rationales

被引：147

作者：

Feuillet, Catherine ^{[1
]}

Leach, Jan E. ^{[2
]}

Rogers, Jane ^{[3
]}

Schnable, Patrick S. ^{[4
]}

Eversole, Kellye ^{[5
]}

机构：

[1] Univ Blaise Pascal, Inst Natl Rech Agron, UMR 1095, F-63100 Clermont Ferrand, France

[2] Colorado State Univ, Dept Bioagr Sci & Pest Management, Ft Collins, CO 80523 USA

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

[4] Iowa State Univ, Ctr Plant Genom, Ames, IA 50011 USA

[5] Evers Associates, Bethesda, MD 20816 USA

来源：

TRENDS IN PLANT SCIENCE | 2011年 / 16卷 / 02期

基金：

英国生物技术与生命科学研究理事会;

关键词：

TRANSCRIPTION FACTOR FAMILY; DISEASE RESISTANCE; DROUGHT TOLERANCE; DRAFT SEQUENCE; PHYSICAL MAP; RICE; GENE; WHEAT; IDENTIFICATION; INTEGRATION;

D O I：

10.1016/j.tplants.2010.10.005

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

2010 marks the 10th anniversary of the completion of the first plant genome sequence (Arabidopsis thaliana). Triggered by advancements in sequencing technologies, many crop genome sequences have been produced, with eight published since 2008. To date, however, only the rice (Oryza sativa) genome sequence has been finished to a quality level similar to that of the Arabidopsis sequence. This trend to produce draft genomes could affect the ability of researchers to address biological questions of speciation and recent evolution or to link sequence variation accurately to phenotypes. Here, we review the current crop genome sequencing activities, discuss how variability in sequence quality impacts utility for different studies and provide a perspective for a paradigm shift in selecting crops for sequencing in the future.

引用

页码：77 / 88

页数：12

共 91 条

[31] The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla [J].

Jaillon, Olivier ;

Aury, Jean-Marc ;

Noel, Benjamin ;

Policriti, Alberto ;

Clepet, Christian ;

Casagrande, Alberto ;

Choisne, Nathalie ;

Aubourg, Sebastien ;

Vitulo, Nicola ;

Jubin, Claire ;

Vezzi, Alessandro ;

Legeai, Fabrice ;

Hugueney, Philippe ;

Dasilva, Corinne ;

Horner, David ;

Mica, Erica ;

Jublot, Delphine ;

Poulain, Julie ;

Bruyère, Clemence ;

Billault, Alain ;

Segurens, Beatrice ;

Gouyvenoux, Michel ;

Ugarte, Edgardo ;

Cattonaro, Federica ;

Anthouard, Veronique ;

Vico, Virginie ;

Del Fabbro, Cristian ;

Alaux, Michael ;

Di Gaspero, Gabriele ;

Dumas, Vincent ;

Felice, Nicoletta ;

Paillard, Sophie ;

Juman, Irena ;

Moroldo, Marco ;

Scalabrin, Simone ;

Canaguier, Aurelie ;

Le Clainche, Isabelle ;

Malacrida, Giorgio ;

Durand, Eleonore ;

Pesole, Graziano ;

Laucou, Valerie ;

Chatelet, Philippe ;

Merdinoglu, Didier ;

Delledonne, Massimo ;

Pezzotti, Mario ;

Lecharny, Alain ;

Scarpelli, Claude ;

Artiguenave, Francois ;

Pè, M. Enrico ;

Valle, Giorgio .

NATURE, 2007, 449 (7161) :463-U5

[32] Towards a better bowl of rice: assigning function to tens of thousands of rice genes [J].

Jung, Ki-Hong ;

An, Gynheung ;

Ronald, Pamela C. .

NATURE REVIEWS GENETICS, 2008, 9 (02) :91-101

[33] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[34] A physical map of the highly heterozygous Populus genome:: integration with the genome sequence and genetic map and analysis of haplotype variation [J].

Kelleher, Colin T. ;

Chiu, Readman ;

Shin, Heesun ;

Bosdet, Ian E. ;

Krzywinski, Martin I. ;

Fjell, Chris D. ;

Wilkin, Jennifer ;

Yin, TongMing ;

DiFazio, Stephen P. ;

Ali, Johar ;

Asano, Jennifer K. ;

Chan, Susanna ;

Cloutier, Alison ;

Girn, Noreen ;

Leach, Stephen ;

Lee, Darlene ;

Mathewson, Carrie A. ;

Olson, Teika ;

O'Connor, Katie ;

Prabhu, Anna-Liisa ;

Smailus, Duane E. ;

Stott, Jeffery M. ;

Tsai, Miranda ;

Wye, Natasja H. ;

Yang, George S. ;

Zhuang, Jun ;

Holt, Robert A. ;

Putnam, Nicholas H. ;

Vrebalov, Julia ;

Giovannoni, James J. ;

Grimwood, Jane ;

Schmutz, Jeremy ;

Rokhsar, Daniel ;

Jones, Steven J. M. ;

Marra, Marco A. ;

Tuskan, Gerald A. ;

Bohlmann, Jorg ;

Ellis, Brian E. ;

Ritland, Kermit ;

Douglas, Carl J. ;

Schein, Jacqueline E. .

PLANT JOURNAL, 2007, 50 (06) :1063-1078

[35] Recent de novo origin of human protein-coding genes [J].

Knowles, David G. ;

McLysaght, Aoife .

GENOME RESEARCH, 2009, 19 (10) :1752-1759

[36] An SNP caused loss of seed shattering during rice domestication [J].

Konishi, Saeko ;

Izawa, Takeshi ;

Lin, Shao Yang ;

Ebana, Kaworu ;

Fukuta, Yoshimichi ;

Sasaki, Takuji ;

Yano, Masahiro .

SCIENCE, 2006, 312 (5778) :1392-1396

[37] Mutant Resources in Rice for Functional Genomics of the Grasses [J].

Krishnan, Arjun ;

Guiderdoni, Emmanuel ;

An, Gynheung ;

Hsing, Yue-ie C. ;

Han, Chang-deok ;

Lee, Myung Chul ;

Yu, Su-May ;

Upadhyaya, Narayana ;

Ramachandran, Srinivasan ;

Zhang, Qifa ;

Sundaresan, Venkatesan ;

Hirochika, Hirohiko ;

Leung, Hei ;

Pereira, Andy .

PLANT PHYSIOLOGY, 2009, 149 (01) :165-170

[38] Allele mining in crops: Prospects and potentials [J].

Kumar, G. Ram ;

Sakthivel, K. ;

Sundaram, R. M. ;

Neeraja, C. N. ;

Balachandran, S. M. ;

Rani, N. Shobha ;

Viraktamath, B. C. ;

Madhav, M. S. .

BIOTECHNOLOGY ADVANCES, 2010, 28 (04) :451-461

[39] Interfamily transfer of a plant pattern-recognition receptor confers broad-spectrum bacterial resistance [J].

Lacombe, Severine ;

Rougon-Cardoso, Alejandra ;

Sherwood, Emma ;

Peeters, Nemo ;

Dahlbeck, Douglas ;

van Esse, H. Peter ;

Smoker, Matthew ;

Rallapalli, Ghanasyam ;

Thomma, Bart P. H. J. ;

Staskawicz, Brian ;

Jones, Jonathan D. G. ;

Zipfel, Cyril .

NATURE BIOTECHNOLOGY, 2010, 28 (04) :365-U94

[40] Enchilada redux: how complete is your genome sequence? [J].

Liu, Renyi ;

Bennetzen, Jeffrey L. .

NEW PHYTOLOGIST, 2008, 179 (02) :249-250

← 1 2 3 4 5 6 7 8 9 10 →