The tomato genome sequence provides insights into fleshy fruit evolution
Shusei Sato
(1)
,
Satoshi Tabata
(1)
,
Hideki Hirakawa
(1)
,
Erika Asamizu
(1)
,
Kenta Shirasawa
(1)
,
Sachiko Isobe
(1)
,
Takakazu Kaneko
(1)
,
Yasukazu Nakamura
(1)
,
Daisuke Shibata
(1)
,
Koh Aoki
(1)
,
Michael Egholm
(2)
,
James Knight
(2)
,
Robert Bogden
(3)
,
Changbao Li
(4, 5)
,
Yang Shuang
(6)
,
Xun Xu
(6)
,
Shengkai Pan
(6)
,
Shifeng Cheng
(6)
,
Xin Liu
(6)
,
Yuanuyan Ren
(6)
,
Jun Wang
(6)
,
Alessandro Albiero
(7)
,
Francesca Dal Pero
(7)
,
Sara Todesco
(7)
,
Joyce van Eck
(8)
,
Robert M. Buels
(8)
,
Aureliano Bombarely
(8)
,
Joseph R. Gosselin
(8)
,
Minyun Huang
(8)
,
Jonathan Leto
(8)
,
Naama Menda
(8)
,
Susan Strickler
(8)
,
Linyong Mao
(8)
,
Shan Gao
(8)
,
Isaak y Tecle
(8)
,
Thomas York
(8)
,
Yi Zheng
(8)
,
Julia T. Vrebalov
(8)
,
Jemin Lee
(8)
,
Silin Zhong
(8)
,
Lukas A. Mueller
(8)
,
Willem J Stiekema
(9)
,
Paolo Ribeca
(10)
,
Tyler Alioto
(10)
,
Wencai Yang
(11)
,
Sanwen Huang
(12)
,
Yongchen Du
(12)
,
Zhonghua Zhang
(12)
,
Jianchang Gao
(12)
,
Yanmei Guo
(12)
,
Xiaosuan Wang
(12)
,
Ying Li
(12)
,
Jun He
(12)
,
Chuanyou Li
(12)
,
Zhukuan Cheng
(12)
,
Jianru Zuo
(12)
,
Jianfeng Ren
(12)
,
Jiuhai Zhao
(12)
,
Liuhua Yan
(12)
,
Hongling Jiang
(12)
,
Bao Wang
(12)
,
Hongshuang Li
(12)
,
Zhenjun Li
(12)
,
Fuyou Fu
(12)
,
Bingtang Chen
(12)
,
Bin Han
(5)
,
Qi Feng
(5)
,
Danlin Fan
(5)
,
Ying Wang
(5)
,
Hongqing Ling
(12, 13)
,
Yongbiao Xue
(12)
,
Doreen Ware
(14)
,
W. Richard Mccombie
(14)
,
Zachary B. Lippmamn
(14)
,
Jer-Ming Chia
(14)
,
Ke Jiang
(14)
,
Shiran Pastermak
(14)
,
Laura Gelley
(14)
,
Melissa Kramer
(14)
,
Lorinda K. Anderson
(15)
,
Song-Bin Chang
(16)
,
Suzanne Royer
(15)
,
Lindsay A. Shearer
(15)
,
Stephen M. Stack
(15)
,
Jocelyn K. C. Rose
(17)
,
Yimin Xu
(17)
,
Nancy Eannetta
(17)
,
Antonio J. Matas
(17)
,
Ryan Mcquinn
(17)
,
Steven D. Tanksley
(17)
,
Francisco Câmara
,
Mathilde M. Causse
(18)
,
Christophe Rothan
(19)
,
Thomas Schiex
(20)
,
Céline Noirot
(20)
,
Arnaud A. Bellec
(21)
,
Christophe Klopp
(20)
,
Helene H. Berges
(21)
,
Jérôme J. Mariette
(20)
,
- Tomato Genome Consortium
1
KDRI -
Kazusa DNA Research Institute
2 454 Life Sciences
3 Amplicon Express Inc.
4 Beijing Academy of Agriculture and Forestry Sciences
5 CAS - Chinese Academy of Sciences
6 BGI - Beijing Genomics Institute [Shenzhen]
7 BMR Genomics S.R.L.
8 Boyce Thompson Institute [Ithaca]
9 Centre for Biosystems Genomics
10 CRG - Centre for Genomic Regulation - Centre de Regulació Genòmica [Barcelona]
11 CAU - China Agricultural University
12 CAAS - Chinese Academy of Agricultural Sciences
13 Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn
14 Cold Spring Harbor
15 CSU - Colorado State University [Fort Collins]
16 National Taiwan University
17 Cornell University [New York]
18 GAFL - Génétique et Amélioration des Fruits et Légumes
19 BFP - Biologie du fruit et pathologie
20 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
21 CNRGV - Centre National de Ressources Génomiques Végétales
2 454 Life Sciences
3 Amplicon Express Inc.
4 Beijing Academy of Agriculture and Forestry Sciences
5 CAS - Chinese Academy of Sciences
6 BGI - Beijing Genomics Institute [Shenzhen]
7 BMR Genomics S.R.L.
8 Boyce Thompson Institute [Ithaca]
9 Centre for Biosystems Genomics
10 CRG - Centre for Genomic Regulation - Centre de Regulació Genòmica [Barcelona]
11 CAU - China Agricultural University
12 CAAS - Chinese Academy of Agricultural Sciences
13 Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn
14 Cold Spring Harbor
15 CSU - Colorado State University [Fort Collins]
16 National Taiwan University
17 Cornell University [New York]
18 GAFL - Génétique et Amélioration des Fruits et Légumes
19 BFP - Biologie du fruit et pathologie
20 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
21 CNRGV - Centre National de Ressources Génomiques Végétales
Xun Xu
- Fonction : Auteur
- PersonId : 801031
- ORCID : 0000-0002-5338-5173
Xin Liu
- Fonction : Auteur
- PersonId : 758866
- ORCID : 0000-0003-3256-2940
Shan Gao
- Fonction : Auteur
- PersonId : 774775
- ORCID : 0000-0001-7424-476X
Ying Li
- Fonction : Auteur
- PersonId : 800973
- ORCID : 0000-0002-3060-9058
Bin Han
- Fonction : Auteur
- PersonId : 15955
- IdHAL : bin-han
- ORCID : 0000-0001-7867-6797
Francisco Câmara
- Fonction : Auteur
Mathilde M. Causse
- Fonction : Auteur
- PersonId : 737384
- IdHAL : mathilde-causse
- ORCID : 0000-0002-0407-4985
- IdRef : 078246423
Christophe Rothan
- Fonction : Auteur
- PersonId : 748402
- IdHAL : crothan
- ORCID : 0000-0002-6831-2823
- IdRef : 033201064
Thomas Schiex
- Fonction : Auteur
- PersonId : 734846
- IdHAL : thomas-schiex
- ORCID : 0000-0001-6049-3415
- IdRef : 057033935
Arnaud A. Bellec
- Fonction : Auteur
- PersonId : 1204910
- IdHAL : bellec-arnaud
- ORCID : 0000-0002-7608-9537
Christophe Klopp
- Fonction : Auteur
- PersonId : 735911
- IdHAL : 0000-0001-7126-5477
- ORCID : 0000-0001-7126-5477
Helene H. Berges
- Fonction : Auteur
- PersonId : 1203296
- ORCID : 0000-0002-5492-1062
Jérôme J. Mariette
- Fonction : Auteur
- PersonId : 14395
- IdHAL : jerome-mariette
- ORCID : 0000-0002-6161-4044
- IdRef : 232567999
- Tomato Genome Consortium
- Fonction : Auteur
Résumé
Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.