The tomato genome sequence provides insights into fleshy fruit evolution

@article{Sato2012TheTG,
  title={The tomato genome sequence provides insights into fleshy fruit evolution},
  author={Shusei Sato and Satoshi Tabata and Hideki Hirakawa and Erika Asamizu and Kenta Shirasawa and Sachiko N Isobe and Takakazu Kaneko and Yasukazu Nakamura and Daisuke Shibata and Koh Aoki and Michael Wayland Egholm and James R. Knight and Robert Bogden and Changbao Li and Yang Shuang and Xun Xu and Shengkai Pan and Shifeng Cheng and Xin Liu and Yuanyuan Ren and Jinjin Wang and Alessandro Albiero and Francesca Dal Pero and Sara Todesco and Joyce van Eck and Robert M. Buels and Aureliano Bombarely and Joseph Gosselin and MIN REN Huang and Jonathan Leto and Naama Menda and Susan R. Strickler and Linyong Mao and Shan Gao and Isaak Y. Tecle and Thomas York and Yi Zheng and Julia T Vrebalov and Je Min Lee and Silin Zhong and Lukas A. Mueller and Willem J. Stiekema and Paolo Ribeca and Tyler S. Alioto and Wencai Yang and Sanwen Huang and Yong-chen Du and Zhonghua Zhang and Jianchang Gao and Yanmei Guo and Xiaoxuan Wang and Youhai Li and Jun He and Chuanyou Li and Zhukuan Cheng and Jianru Zuo and Jianfeng Ren and Jiuhai Zhao and Liuhua Yan and Hongling Jiang and Baoliang Wang and Hongshuang Li and Zhenjun Li and Fuyou Fu and Bingtang Chen and Bin Han and Qi Feng and Danlin Fan and Ying Wang and Hong-Qing Ling and Yongbiao Xue and Doreen H Ware and W. Richard McCombie and Zachary B. Lippman and Jer-Ming Chia and Ke Jiang and Shiran Pasternak and Laura Gelley and Melissa Kramer and Lorinda K. Anderson and Song-Bin Chang and Suzanne M. Royer and Lindsay A. Shearer and Steph{\^e}n M. Stack and Jocelyn K. C. Rose and Yimin Xu and Nancy T. Eannetta and Antonio J. Matas and Ryan P. McQuinn and Steven D. Tanksley and Francisco Camara and Roderic Guig{\'o} and Stephane Rombauts and Jeffrey A. Fawcett and Yves Van de Peer and Dani Zamir and Chunbo Liang and Manuel Spannagl and Heidrun Gundlach and R{\'e}my Bruggmann and Klaus F. X. Mayer and Zhiqi Jia and Junhong Zhang and Zhibiao Ye and Gerard J. Bishop and Sarah A. Butcher and Rosa M Lopez-Cobollo and Daniel W. A. Buchan and Ioannis Filippis and James C. Abbott and Rekha Dixit and Manju Singh and Archana Singh and Jitendra Kumar Pal and Awadhesh Pandit and Pradeep K. Singh and Ajay K. Mahato and Vivek Dogra and Kishor Gaikwad and Tilak Raj Sharma and Trilochan Mohapatra and Nagendra Kumar Singh and Mathilde Causse and Christophe Rothan and T. Schiex and C{\'e}line Noirot and Arnaud Bellec and Christophe Klopp and Corinne Delalande and H{\'e}l{\`e}ne Berg{\`e}s and J{\'e}r{\^o}me Mariette and Pierre Frasse and Sonia Vautrin and Mohamed Zouine and Alain Latché and Christine M. Rousseau and Farid Regad and J. C. Pech and Murielle Philippot and Mondher Bouzayen and Pierre Pericard and Sonia Osorio and Asun Fern{\'a}ndez del Carmen and Antonio Jos{\'e} Monforte and Antonio Granell and Rafael Fern{\'a}ndez-Mu{\~n}oz and Mariana Conte and Gabriela Lichtenstein and Fernando Carrari and Gianluca De Bellis and Fabio Fuligni and Clelia Peano and Silvana Grandillo and Pasquale Termolino and Marco Pietrella and Elio Fantini and Giulia Falcone and Alessia Fiore and Giovanni Giuliano and Loredana Lopez and Paolo Facella and Gaetano Perrotta and Loretta Daddiego and Glenn J Bryan and Modesto Orozco and Xavier Pastor and David Torrents and Keygene N. V. Marco G. M. van Schriek and Richard M. C. Feron and Jan van Oeveren and Pieter de Heer and Lorena daPonte and Saskia Jacobs-Oomen and Michael Cariaso and Marcel Prins and Michiel JT van Eijk and Antoine Janssen and Mark van Haaren and Sung-Hwan Jo and Jungeun Kim and Suk-Yoon. Kwon and Sangmi Kim and Dal-Hoe Koo and Sanghyeob Lee and Cheol-Goo Hur and Chris Clouser and Alain Rico and Asis Hallab and Christiane Gebhardt and Kathrin Klee and Anika J{\"o}cker and Jens Warfsmann and Ulrike Goebel and Shingo Kawamura and Kentaro Yano and Jamie Sherman and Hiroyuki Fukuoka and Satomi Negoro and Sarita Bhutty and Parul Chowdhury and Debasis Chattopadhyay and Erwin Datema and Sandra Smit and Elio Schijlen and Jos{\'e} van de Belt and Jan C. van Haarst and Sander Peters and Marjo J. van Staveren and Marleen H. C. Henkens and Paul Mooyman and Thamara Hesselink and Roeland C. H. J. van Ham and Guoyong Jiang and Marcus Droege and Doil Choi and Byung-Cheol Kang and Byung-Dong Kim and Minkyu Park and Seungil Kim and Seon-In Yeom and Yong-Hwan Lee and Yang Do Choi and Guang-cun Li and Jianwei Gao and Yongsheng Liu and Shengxiong Huang and Victoria Fern{\'a}ndez-Pedrosa and Carmen Collado and Sheila Zuniga and Guoping Wang and Rebecca M. Cade and Robert A. Dietrich and Jane Rogers and Sandra Knapp and Zhangjun Fei and Ruth White and Theodore W. Thannhauser and James J. Giovannoni and Miguel Angel Botella and Louise Gilbert and Ramón Gerardo Guevara González and Jose Luis Goicoechea and Yeisoo Yu and Dave Kudrna and Kristi Collura and Marina Wissotski and Rod A. Wing and Heiko Schoof and Blake C. Meyers and Aishwarya Bala Gurazada and Pamela J. Green and Saloni Mathur and Shailendra Vyas and Amol Kumar U. Solanke and Rahul Kumar and Vikrant Gupta and Arun Kumar Sharma and Paramjit Khurana and Jitendra P. Khurana and Akhilesh Kumar Tyagi and Tam{\'a}s Dalmay and Irina Mohorianu and Brandon Walts and Srikar Chamala and William Brad Barbazuk and Jingping Li and Hui Guo and Taeho Lee and Yupeng Wang and Dong Zhang and Andrew H. Paterson and Xiyin Wang and Haibao Tang and Amalia Barone and Maria Luisa Chiusano and Maria Raffaella Ercolano and Nunzio D’Agostino and Miriam Di Filippo and Alessandra Traini and Walter Sanseverino and Luigi Frusciante and Graham B. Seymour and Mounir Elharam and Ying Fu and Axin Hua and Steve Kenton and Jennifer A. Lewis and Shao Ping Lin and Fares Najar and Hongshing Lai and Baifang Qin and Chunmei Qu and Ruihua Shi and Doug White and James R. White and Yanbo Xing and Keqin Yang and Jing Yi and Ziyun Yao and Liping Zhou and B. A. Roe and Alessandro Vezzi and M Dangelo and Rosanna Zimbello and Riccardo Schiavon and Elisa Caniato and Chiara Rigobello and David J. Campagna and Nicola Vitulo and Giorgio Valle and David R. Nelson and Emanuele De Paoli and D{\'o}ra Szinay and Hans de Jong and Yuling Bai and R. Visser and Rene Klein Lankhorst and Helen Beasley and Karen McLaren and Christine M. Nicholson and Clare Riddle and Giulio Gianese},
  journal={Nature},
  year={2012},
  volume={485},
  pages={635 - 641}
}
Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera 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, 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… Expand
Advances in tomato research in the post-genome era
TLDR
An overview of the origins of tomato and its position in the wider Solanaceae is provided, and the impact of the tomato genome sequence onSolanaceae research is demonstrated on the basis of recent literature that has made use of this new resource. Expand
Characterization the complete chloroplast genome of the tomato (Solanum lycopersicum L.) from China
TLDR
The phylogenetic relationship analysis using Maximum Likelihood method showed that tomato (Solanum lycopersicum L.) much closely related to two kinds of wild tomatoes Solanum pimpinellifolium and SolAnum cheesmaniae. Expand
Tomato Resources for Functional Genomics
TLDR
The present chapter will describe the main resources, strategies and tools currently available for linking genes to phenotype in tomato. Expand
Tomato Genome Sequence
TLDR
The reference genome sequence is derived from Solanum lycopersicum cv. Expand
Guidelines to use tomato in experiments with a controlled environment
TLDR
Tomato is widely used as a model crop for fruit development but also for diverse physiological, cellular, biochemical, molecular, and genetic studies, and using appropriate cultivation techniques makes tomato a convenient model plant for researchers, even for beginners. Expand
From randomly to inevitable: Accelerating tomato breeding by comprehensive tools and information
  • H. Ezura
  • Biology, Medicine
  • Breeding science
  • 2013
TLDR
Five review articles report the comprehensive tools and information that are changing tomato breeding from a random effort to inevitable research and contribute to the rapid and efficient breeding of tomato and also to fleshy fruit research. Expand
Population Genomics of Tomato
TLDR
The study of these genomes confirmed the new phylogenetic organization of the tomato clade, Solanum section Lycopersicon, composed of 13 species, and the molecular mechanisms of adaptation to abiotic stress in cultivated and wild tomato species. Expand
The genome of the stress-tolerant wild tomato species Solanum pennellii
TLDR
A high-quality genome assembly of the parents of the IL population of S. pennellii is described, defining candidate genes for stress tolerance and providing evidence that transposable elements had a role in the evolution of these traits. Expand
A Solanum lycopersicoides reference genome facilitates biological discovery in tomato
TLDR
The genome sequence and IL map will support the development of S. lycopersicoides as a model for studying fruit nutrient/quality, pathogen resistance, and environmental stress tolerance traits that have been identified in the IL population and are known to exist in S. Lycopericoides. Expand
Trait discovery and editing in tomato
TLDR
Insight is provided into the major tomato traits and underlying causal genetic variations discovered so far and the existing genetic resources and most recent strategies for trait discovery in tomato and the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing are explored. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 247 REFERENCES
Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes
TLDR
A first contribution toward deciphering the genetic information of tomato is presented, presenting the complete sequence of the tomato chloroplast genome (plastome), and several new sites of RNA editing by cytidine-to-uridine conversion are discovered. Expand
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
TLDR
A first genome-wide analysis of these two species, based on two large collections of BAC end sequences, presents a first glimpse into the evolution of Solanaceous genomes, both within the family and relative to other plant species. Expand
The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond1
TLDR
The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond. Expand
Genome sequence and analysis of the tuber crop potato
TLDR
The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin. Expand
Chromosomal evolution in the plant family Solanaceae
TLDR
The Solanaceae has experienced chromosomal changes at a modest rate compared with other families and the rates are likely conserved across different lineages of the family. Expand
High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes
TLDR
The mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species allows the first syntenic comparison between species from these two families and provides new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae. Expand
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
TLDR
A high-quality draft of the genome sequence of grapevine is obtained from a highly homozygous genotype, revealing the contribution of three ancestral genomes to the grapevine haploid content and explaining the chronology of previously described whole-genome duplication events in the evolution of flowering plants. Expand
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
TLDR
The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies and aid in tomato functional genomics and molecular breeding. Expand
A Snapshot of the Emerging Tomato Genome Sequence
TLDR
This first snapshot of the emerging tomato genome and its annotation is presented, a short comparison with potato sequence data, and the tools available for the researchers to exploit this new resource are presented. Expand
Structural Differences in Chromosomes Distinguish Species in the Tomato Clade
TLDR
A number of unexpected synaptic configurations such as mismatched kinetochores, inversion loops and reciprocal translocations are revealed that substantial changes in chromosome structure have occurred among species within the tomato clade. Expand
...
1
2
3
4
5
...