The genome of woodland strawberry (Fragaria vesca)

被引：887

作者：

Shulaev, Vladimir ^{[2
]}

Sargent, Daniel J.

Crowhurst, Ross N. ^{[3
]}

Mockler, Todd C. ^{[4
,5
]}

Folkerts, Otto ^{[6
]}

Delcher, Arthur L. ^{[7
]}

Jaiswal, Pankaj ^{[4
]}

Mockaitis, Keithanne ^{[8
]}

Liston, Aaron ^{[4
]}

Mane, Shrinivasrao P. ^{[9
]}

Burns, Paul ^{[10
]}

Davis, Thomas M. ^{[11
]}

Slovin, Janet P. ^{[12
]}

Bassil, Nahla ^{[13
]}

Hellens, Roger P. ^{[3
]}

Evans, Clive ^{[9
]}

Harkins, Tim ^{[14
]}

Kodira, Chinnappa ^{[14
]}

Desany, Brian ^{[14
]}

Crasta, Oswald R. ^{[6
]}

Jensen, Roderick V. ^{[15
]}

Allan, Andrew C. ^{[3
,16
]}

Michael, Todd P. ^{[17
]}

Setubal, Joao Carlos ^{[9
,18
]}

Celton, Jean-Marc ^{[19
]}

Rees, D. Jasper G. ^{[19
]}

Williams, Kelly P. ^{[9
]}

Holt, Sarah H. ^{[20
,21
]}

Rojas, Juan Jairo Ruiz ^{[20
]}

Chatterjee, Mithu ^{[1
,22
]}

Liu, Bo ^{[11
]}

Silva, Herman ^{[23
]}

Meisel, Lee ^{[24
]}

Adato, Avital ^{[25
]}

Filichkin, Sergei A. ^{[4
,5
]}

Troggio, Michela ^{[26
]}

Viola, Roberto ^{[26
]}

Ashman, Tia-Lynn ^{[27
]}

Wang, Hao ^{[28
]}

Dharmawardhana, Palitha ^{[4
]}

Elser, Justin ^{[4
]}

Raja, Rajani ^{[4
]}

Priest, Henry D. ^{[4
,5
]}

Bryant, Douglas W., Jr. ^{[4
,5
]}

Fox, Samuel E. ^{[4
,5
]}

Givan, Scott A. ^{[4
,5
]}

Wilhelm, Larry J. ^{[4
,5
]}

Naithani, Sushma ^{[29
]}

Christoffels, Alan ^{[30
]}

Salama, David Y. ^{[1
]}

机构：

[1] Univ Florida, Dept Hort Sci, Gainesville, FL 32611 USA

[2] Univ N Texas, Dept Biol Sci, Denton, TX 76203 USA

[3] New Zealand Inst Plant & Food Res Ltd Plant & Foo, Mt Albert Res Ctr, Auckland, New Zealand

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

[5] Oregon State Univ, CGRB, Corvallis, OR 97331 USA

[6] Chromatin Inc, Champaign, IL USA

[7] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA

[8] Indiana Univ, Ctr Genom & Bioinformat, Bloomington, IN USA

[9] Virginia Polytech Inst & State Univ, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA

[10] Joint Georgia Tech & Emory Wallace H Coulter Dept, Atlanta, GA USA

[11] Univ New Hampshire, Dept Biol Sci, Durham, NH 03824 USA

[12] ARS, USDA, Henry Wallace Beltsville Agr Res Ctr, Beltsville, MD USA

[13] ARS, USDA, Corvallis, OR USA

[14] Roche Appl Sci, Roche Diagnost, Indianapolis, IN USA

[15] Virginia Tech, Dept Biol Sci, Blacksburg, VA USA

[16] Univ Auckland, Sch Biol Sci, Auckland 1, New Zealand

[17] Rutgers State Univ, Waksman Inst Microbiol, Piscataway, NJ 08855 USA

[18] Virginia Tech, Dept Comp Sci, Blacksburg, VA USA

[19] Univ Western Cape, Dept Biotechnol, ZA-7535 Bellville, South Africa

[20] Virginia Polytech Inst & State Univ, Dept Hort, Blacksburg, VA 24061 USA

[21] Inst Adv Learning & Res, Inst Sustainable & Renewable Resources, Danville, PA USA

[22] Univ Florida, Grad Program Plant Mol & Cellular Biol, Gainesville, FL USA

[23] Univ Chile, Fac Agron, Santiago, Chile

[24] Univ Andres Bello, Fac Ciencias Biol, Ctr Biotecnol Vegetal, Santiago, Chile

[25] Weizmann Inst Sci, Dept Plant Sci, IL-76100 Rehovot, Israel

[26] Fdn Edmund Mach, Res & Innovat Ctr, IASMA, San Michele All Adige, Trento, Italy

[27] Univ Pittsburgh, Dept Biol Sci, Pittsburgh, PA 15260 USA

[28] Univ Georgia, Dept Genet, Athens, GA 30602 USA

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

[30] Univ Western Cape, S African Natl Bioinformat Inst, ZA-7535 Bellville, South Africa

[31] Tech Univ Munich, D-8000 Munich, Germany

[32] Univ Illinois, Dept Nat Resources & Environm Sci, Urbana, IL 61801 USA

[33] Norwegian Inst Agr & Environm Res, Kvithamar, Stjordal, Norway

[34] IRTA, Barcelona, Spain

[35] Ctr Recerca Agrigenom CSIC IRTA UAB, Barcelona, Spain

[36] INRA, UREF, Villenave Dornon, France

[37] Georgia Tech, Sch Computat Sci & Engn, Atlanta, GA USA

来源：

NATURE GENETICS | 2011年 / 43卷 / 02期

基金：

美国国家卫生研究院; 美国农业部; 英国生物技术与生命科学研究理事会; 美国国家科学基金会;

关键词：

PHYLOGENETIC TREE SELECTION; DIPLOID STRAWBERRY; GENE-EXPRESSION; SEQUENCE; ALIGNMENT; PROTEINS; ROSACEAE; PLANTS; IDENTIFICATION; TRANSFORMATION;

D O I：

10.1038/ng.740

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria x ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to x39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.

引用

页码：109 / 116

页数：8

共 61 条

[1] Gene expression analysis of strawberry achene and receptacle maturation using DNA microarrays
Aharoni, A
O'Connell, AP
[J]. JOURNAL OF EXPERIMENTAL BOTANY, 2002, 53 (377) : 2073 - 2087
[2] Appropriate choice of antibiotic and Agrobacterium strain improves transformation of anti biotic-sensitive Fragaria vesca and F-v. semperflorens
Alsheikh, MK
Suso, HP
Robson, M
Battey, NH
Wetten, A
[J]. PLANT CELL REPORTS, 2002, 20 (12) : 1173 - 1180
[3] 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
[4] Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome
Baucom, Regina S.
Estill, James C.
Chaparro, Cristian
Upshaw, Naadira
Jogi, Ansuya
Deragon, Jean-Marc
Westerman, Richard P.
SanMiguel, Phillip J.
Bennetzen, Jeffrey L.
[J]. PLOS GENETICS, 2009, 5 (11):
[5] Supersplat-spliced RNA-seq alignment
Bryant, Douglas W., Jr.
Shen, Rongkun
Priest, Henry D.
Wong, Weng-Keen
Mockler, Todd C.
[J]. BIOINFORMATICS, 2010, 26 (12) : 1500 - 1505
[6] Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers
Cabrera, Antonio
Kozik, Alex
Howad, Werner
Arus, Pere
Iezzoni, Amy F.
van der Knaap, Esther
[J]. BMC GENOMICS, 2009, 10
[7] The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications -: art. no. 20
Choisne, N
Demange, N
Orjeda, G
Samain, S
D'Hont, A
Cattolico, L
Pelletier, E
Couloux, A
Segurens, B
Wincker, P
Scarpelli, C
Weissenbach, J
Salanoubat, M
Quétier, F
Singh, NK
Mohapatra, T
Sharma, TR
Gaikwad, K
Singh, A
Dalal, V
Srivastava, SK
Dixit, A
Pal, AK
Ghazi, IA
Yadav, M
Pandit, A
Bhargava, A
Sureshbabu, K
Dixit, R
Singh, H
Swain, SC
Pal, S
Ragiba, M
Singh, PK
Singhal, V
Mendiratta, SD
Batra, K
Raghuvanshi, S
Mohanty, A
Bharti, AK
Gaur, A
Gupta, V
Kumar, D
Vydianathan, R
Vij, S
Kapur, A
Khurana, P
Sharma, S
Khurana, P
Khurana, JP
[J]. BMC BIOLOGY, 2005, 3 (1)
[8] The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales:: RNA editing and multiple losses of a group II intron
Daniell, Henry
Wurdack, Kenneth J.
Kanagaraj, Anderson
Lee, Seung-Bum
Saski, Christopher
Jansen, Robert K.
[J]. THEORETICAL AND APPLIED GENETICS, 2008, 116 (05) : 723 - 737
[9] Darrow G.M., 1966, History, breeding and physiology. The strawberry.History
[10] An examination of targeted gene neighborhoods in strawberry
Davis, Thomas M.
Shields, Melanie E.
Zhang, Qian
Tombolato-Terzic, Denise
Bennetzen, Jeffrey L.
Pontaroli, Ana C.
Wang, Hao
Yao, Qin
SanMiguel, Phillip
Folta, Kevin M.
[J]. BMC PLANT BIOLOGY, 2010, 10

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