The Plant Genome (Mar 2009)

A Snapshot of the Emerging Tomato Genome Sequence

  • Lukas A. Mueller,
  • René Klein Lankhorst,
  • Steven D. Tanksley,
  • James J. Giovannoni,
  • Ruth White,
  • Julia Vrebalov,
  • Zhangjun Fei,
  • Joyce van Eck,
  • Robert Buels,
  • Adri A. Mills,
  • Naama Menda,
  • Isaak Y. Tecle,
  • Aureliano Bombarely,
  • Stephen Stack,
  • Suzanne M. Royer,
  • Song-Bin Chang,
  • Lindsay A. Shearer,
  • Byung Dong Kim,
  • Sung-Hwan Jo,
  • Cheol-Goo Hur,
  • Doil Choi,
  • Chang-Bao Li,
  • Jiuhai Zhao,
  • Hongling Jiang,
  • Yu Geng,
  • Yuanyuan Dai,
  • Huajie Fan,
  • Jinfeng Chen,
  • Fei Lu,
  • Jinfeng Shi,
  • Shouhong Sun,
  • Jianjun Chen,
  • Xiaohua Yang,
  • Chen Lu,
  • Mingsheng Chen,
  • Zhukuan Cheng,
  • Chuanyou Li,
  • Hongqing Ling,
  • Yongbiao Xue,
  • Ying Wang,
  • Graham B. Seymour,
  • Gerard J. Bishop,
  • Glenn Bryan,
  • Jane Rogers,
  • Sarah Sims,
  • Sarah Butcher,
  • Daniel Buchan,
  • James Abbott,
  • Helen Beasley,
  • Christine Nicholson,
  • Clare Riddle,
  • Sean Humphray,
  • Karen McLaren,
  • Saloni Mathur,
  • Shailendra Vyas,
  • Amolkumar U. Solanke,
  • Rahul Kumar,
  • Vikrant Gupta,
  • Arun K. Sharma,
  • Paramjit Khurana,
  • Jitendra P. Khurana,
  • Akhilesh Tyagi,
  • Sarita,
  • Parul Chowdhury,
  • Smriti Shridhar,
  • Debasis Chattopadhyay,
  • Awadhesh Pandit,
  • Pradeep Singh,
  • Ajay Kumar,
  • Rekha Dixit,
  • Archana Singh,
  • Sumera Praveen,
  • Vivek Dalal,
  • Mahavir Yadav,
  • Irfan Ahmad Ghazi,
  • Kishor Gaikwad,
  • Tilak Raj Sharma,
  • Trilochan Mohapatra,
  • Nagendra Kumar Singh,
  • Dóra Szinay,
  • Hans de Jong,
  • Sander Peters,
  • Marjo van Staveren,
  • Erwin Datema,
  • Mark W.E.J. Fiers,
  • Roeland C.H.J. van Ham,
  • P. Lindhout,
  • Murielle Philippot,
  • Pierre Frasse,
  • Farid Regad,
  • Mohamed Zouine,
  • Mondher Bouzayen,
  • Erika Asamizu,
  • Shusei Sato,
  • Hiroyuki Fukuoka,
  • Satoshi Tabata,
  • Daisuke Shibata,
  • Miguel A. Botella,
  • M. Perez-Alonso,
  • V. Fernandez-Pedrosa,
  • Sonia Osorio,
  • Amparo Mico,
  • Antonio Granell,
  • Zhonghua Zhang,
  • Jun He,
  • Sanwen Huang,
  • Yongchen Du,
  • Dongyu Qu,
  • Longfei Liu,
  • Dongyuan Liu,
  • Jun Wang,
  • Zhibiao Ye,
  • Wencai Yang,
  • Guoping Wang,
  • Alessandro Vezzi,
  • Sara Todesco,
  • Giorgio Valle,
  • Giulia Falcone,
  • Marco Pietrella,
  • Giovanni Giuliano,
  • Silvana Grandillo,
  • Alessandra Traini,
  • Nunzio D'Agostino,
  • Maria Luisa Chiusano,
  • Mara Ercolano,
  • Amalia Barone,
  • Luigi Frusciante,
  • Heiko Schoof,
  • Anika Jöcker,
  • Rémy Bruggmann,
  • Manuel Spannagl,
  • Klaus X.F. Mayer,
  • Roderic Guigó,
  • Francisco Camara,
  • Stephane Rombauts,
  • Jeffrey A. Fawcett,
  • Yves Van de Peer,
  • Sandra Knapp,
  • Dani Zamir,
  • Willem Stiekema

DOI
https://doi.org/10.3835/plantgenome2008.08.0005
Journal volume & issue
Vol. 2, no. 1
pp. 78 – 92

Abstract

Read online

The genome of tomato ( L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.