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This article in TPG

  1. Vol. 2 No. 1, p. 78-92
    unlockOPEN ACCESS
     
    Received: Aug 21, 2008
    Accepted: Mar 18, 2009


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doi:10.3835/plantgenome2008.08.0005

A Snapshot of the Emerging Tomato Genome Sequence

  1. Lukas A. Mueller ,
  2. René Klein Lankhorst,
  3. Steven D. Tanksley,
  4. James J. Giovannoni,
  5. Ruth White,
  6. Julia Vrebalov,
  7. Zhangjun Fei,
  8. Joyce van Eck,
  9. Robert Buels,
  10. Adri A. Mills,
  11. Naama Menda,
  12. Isaak Y. Tecle,
  13. Aureliano Bombarely,
  14. Stephen Stack,
  15. Suzanne M. Royer,
  16. Song-Bin Chang,
  17. Lindsay A. Shearer,
  18. Byung Dong Kim,
  19. Sung-Hwan Jo,
  20. Cheol-Goo Hur,
  21. Doil Choi,
  22. Chang-Bao Li,
  23. Jiuhai Zhao,
  24. Hongling Jiang,
  25. Yu Geng,
  26. Yuanyuan Dai,
  27. Huajie Fan,
  28. Jinfeng Chen,
  29. Fei Lu,
  30. Jinfeng Shi,
  31. Shouhong Sun,
  32. Jianjun Chen,
  33. Xiaohua Yang,
  34. Chen Lu,
  35. Mingsheng Chen,
  36. Zhukuan Cheng,
  37. Chuanyou Li,
  38. Hongqing Ling,
  39. Yongbiao Xue,
  40. Ying Wang,
  41. Graham B. Seymour,
  42. Gerard J. Bishop,
  43. Glenn Bryan,
  44. Jane Rogers,
  45. Sarah Sims,
  46. Sarah Butcher,
  47. Daniel Buchan,
  48. James Abbott,
  49. Helen Beasley,
  50. Christine Nicholson,
  51. Clare Riddle,
  52. Sean Humphray,
  53. Karen McLaren,
  54. Saloni Mathur,
  55. Shailendra Vyas,
  56. Amolkumar U. Solanke,
  57. Rahul Kumar,
  58. Vikrant Gupta,
  59. Arun K. Sharma,
  60. Paramjit Khurana,
  61. Jitendra P. Khurana,
  62. Akhilesh Tyagi,
  63.  Sarita,
  64. Parul Chowdhury,
  65. Smriti Shridhar,
  66. Debasis Chattopadhyay,
  67. Awadhesh Pandit,
  68. Pradeep Singh,
  69. Ajay Kumar,
  70. Rekha Dixit,
  71. Archana Singh,
  72. Sumera Praveen,
  73. Vivek Dalal,
  74. Mahavir Yadav,
  75. Irfan Ahmad Ghazi,
  76. Kishor Gaikwad,
  77. Tilak Raj Sharma,
  78. Trilochan Mohapatra,
  79. Nagendra Kumar Singh,
  80. Dóra Szinay,
  81. Hans de Jong,
  82. Sander Peters,
  83. Marjo van Staveren,
  84. Erwin Datema,
  85. Mark W.E.J. Fiers,
  86. Roeland C.H.J. van Ham,
  87. P. Lindhout,
  88. Murielle Philippot,
  89. Pierre Frasse,
  90. Farid Regad,
  91. Mohamed Zouine,
  92. Mondher Bouzayen,
  93. Erika Asamizu,
  94. Shusei Sato,
  95. Hiroyuki Fukuoka,
  96. Satoshi Tabata,
  97. Daisuke Shibata,
  98. Miguel A. Botella,
  99. M. Perez-Alonso,
  100. V. Fernandez-Pedrosa,
  101. Sonia Osorio,
  102. Amparo Mico,
  103. Antonio Granell,
  104. Zhonghua Zhang,
  105. Jun He,
  106. Sanwen Huang,
  107. Yongchen Du,
  108. Dongyu Qu,
  109. Longfei Liu,
  110. Dongyuan Liu,
  111. Jun Wang,
  112. Zhibiao Ye,
  113. Wencai Yang,
  114. Guoping Wang,
  115. Alessandro Vezzi,
  116. Sara Todesco,
  117. Giorgio Valle,
  118. Giulia Falcone,
  119. Marco Pietrella,
  120. Giovanni Giuliano,
  121. Silvana Grandillo,
  122. Alessandra Traini,
  123. Nunzio D'Agostino,
  124. Maria Luisa Chiusano,
  125. Mara Ercolano,
  126. Amalia Barone,
  127. Luigi Frusciante,
  128. Heiko Schoof,
  129. Anika Jöcker,
  130. Rémy Bruggmann,
  131. Manuel Spannagl,
  132. Klaus X.F. Mayer,
  133. Roderic Guigó,
  134. Francisco Camara,
  135. Stephane Rombauts,
  136. Jeffrey A. Fawcett,
  137. Yves Van de Peer,
  138. Sandra Knapp,
  139. Dani Zamir and
  140. Willem Stiekema
  1. L.A. Mueller, J.J. Giovannoni, R. White, J. Vrebalov, Z. Fei, J. van Eck, R. Buels, A. Mills, N. Menda, I.Y. Tecle, and A. Bombarely, Boyce Thompson Institute, Ithaca, NY 14853; S.D. Tanksley, Dep. Plant Breeding, Cornell Univ., Ithaca, NY 14853; S. Stack, S.M. Royer, S.-B. Chang, and L.A. Shearer, Dep. of Biology, Colorado State Univ., Fort Collins, CO 80523; S.-H. Jo and C.-G. Hur, Plant Genome Research Center, KRIBB, Taejon 305-600, Korea; B.D. Kim and D. Choi, Seoul National Univ., San 56-1 Shinlim-dong, Gwanak-gu, Seoul 151-742, Korea. C.-B. Li, J. Zhao, H. Jiang, Y. Geng, Y. Dai, H. Fan, J. Chen, F. Lu, J. Shi, S. Sun, J. Chen, X. Yang, C. Lu, M. Chen, Z. Cheng, C. Li, H. Ling, Y. Xue, and Y. Wang, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; G. Seymour, Division of Plant Sciences, Univ. of Nottingham, Sutton Bonington, LE12 5RD, UK; G.J. Bishop, S. Butcher, D. Buchan, and J. Abbott, Imperial College London, London, SW7 2AZ, UK; G. Bryan, SCRI Invergowrie, Dundee, DD2 5DA, UK; S. Mathur, S. Vyas, A.U. Solanke, R. Kumar, V. Gupta, A.K. Sharma, P. Khurana, J.P. Khurana, and A. Tyagi, Univ. of Delhi South Campus, New Delhi, 110 02, India; Sarita, P. Chowdhury, S. Shridhar, and D. Chattopadhyay, National Institute for Plant Genome Research, New Delhi, 110 067, India; A. Pandit, P. Singh, A. Kumar, R. Dixit, A. Singh, S. Praveen, V. Dalal, M. Yadav, I.A. Ghazi, K. Gaikwad, T.R. Sharma, T. Mohapatra, and N.K. Singh, NRC on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012, India; R. Klein Lankhorst, R.C.H.J. van Ham, and W. Stiekema, Centre for BioSystems Genomics, P.O. Box 98, 6700 AB, Wageningen, Netherlands; D. Szinay, H. de Jong, S. Peters, and P. Lindhout, Wageningen Univ., Lab. of Genetics, Arboretumlaan 4, 6703 BD, Wageningen, Netherlands; M. van Staveren, E. Datema, M.W.E.J. Fiers, and R.C.H.J. van Ham, Plant Research International, Droevendaalsesteeg 1, 6708 PB, Wageningen, Netherlands; M. Philippot, P. Frasse, F. Regad, M. Zouine, and M. Bouzayen, UMR990, INRA, chemin de Borde Rouge, 31326 Castanet-Tolosane, France; E. Asamizu, S. Sato, S. Tabata, and D. Shibata, Kazusa, Kisarazu, 292-0818, Chiba, Japan; S. Osorio, A. Mico, and A. Granell, Instituto de Biología Molecular y Celular de Plantas, CSIC/Universidad Politécnica de Valencia Ciudad Politécnica de la Innovación - Edificio 8E, 46 011 Valencia, Spain; M.A. Botella, Univ. of Málaga, Campus de Teatinos, 29071 Málaga, Spain; G. Falcone, M. Pietrella, and G. Giuliano, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy; A. Traini, N. D'Agostino, M.L. Chiusano, M. Ercolano, A. Barone, and L. Frusciante, Dep. of Soil, Plant, Environmental and Animal Production Sciences, Univ. of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; D. Zamir, Hebrew Univ., P.O. Box 12, Rehovot 76100, Israel; H. Fukuoka, National Institute of Vegetable and Tea Science, National Agriculture Research Organization, 360 Kusawa, Ano-cho, Tsu-shi, Mie 514-2392, Japan (NIVTS); J. Rogers, S. Sims, H. Beasley, C. Nicholson, C. Riddle, and K. McLaren, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK; Z. Zhang, J. He, S. Huang, Y. Du, and D. Qu, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; L. Liu, D. Liu, and J. Wang, Beijing Genomics Institute, Shenzhen 518083, China; Z. Ye, College of Horticulture and Forestry, Huazhong Agricultural Univ., Wuhan, China; W. Yang, College of Agronomy and Biotechnology, China Agricultural Univ., Beijing 100094, China; G. Wang, Dep. of Horticulture, South China Agricultural Univ., Guangzhou, China; H. Schoof and A. Jöcker, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; M. Perez-Alonso and V. Fernandez-Pedrosa, Sistemas Genómicos, SL, Avenida Benjamín Franklin, 46980 Paterna, Valencia, Spain; R. Guigó and F. Camara, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003 Barcelona, Spain; S. Humphray, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Saffron Walden, Essex, CB10 1XL, UK; S. Rombauts, J.A. Fawcett, and Y. van de Peer, VIB/Ghent Univ., Technologiepark 927, 9052 Ghent, Belgium; S. Knapp, Botany Dep., The Natural History Museum, Cromwell Rd., London, SW7 5BD, UK; R. Bruggmann, Rutgers, The State Univ. of New Jersey, Waksman Institute of Microbiology, 190 Frelinghuysen Rd., Piscataway, NJ 08854-8020; M. Spannagl and K.X.F. Mayer, MIPS/Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; A. Vezzi, S. Todesco, and G. Valle, CRIBI, Univ. of Padua, via U. Bassi, 58/b-35131 Padua, Italy; S. Grandillo, CNR, Institute for Plant Genetics, Portici, Via Università 133, 80055 Portici, Italy; L.A. Mueller, Z. Fei, R. Buels, C.-G. Hur, D. Buchan, S. Mathur, E. Datema, M.W.E.J. Fiers, A. Traini, N. D'Agostino, M.L. Chiusano, H. Schoof, A. Jöcker, R. Bruggmann, M. Spannagl, K.X.F. Mayer, R. Guigó, F. Camara, S. Rombauts, J.A. Fawcett, and Y. van de Peer, International Tomato Genome Annotation Group (ITAG); J.J. Giovannoni and R. White, USDA- ARS, Tower Road, Ithaca, NY 14853, USA.

Abstract

The genome of tomato (Solanum lycopersicum 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 (Solanum tuberosum 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.

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