A snapshot of the emerging tomato genome sequence

L.A. Mueller, R.M. Klein Lankhorst, S.D. Tanksley, R.M. Peters, M.J. van Staveren, E. Datema, M.W.E.J. Fiers, R.C.H.J. van Ham, D. Szinay, J.H.S.G.M. de Jong

Research output: Contribution to journalArticleAcademicpeer-review

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
Original languageEnglish
Pages (from-to)78-92
JournalThe Plant Genome
Volume2
Issue number1
DOIs
Publication statusPublished - 2009

Fingerprint

Lycopersicon esculentum
tomatoes
Genome
genome
Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Solanaceae
Solanum tuberosum
Euchromatin
Nucleic Acid Databases
Firearms
Solanum lycopersicum
Korea
Systems Analysis
Genomics
Netherlands
Spain
Italy
France
United Kingdom

Cite this

Mueller, L.A. ; Klein Lankhorst, R.M. ; Tanksley, S.D. ; Peters, R.M. ; van Staveren, M.J. ; Datema, E. ; Fiers, M.W.E.J. ; van Ham, R.C.H.J. ; Szinay, D. ; de Jong, J.H.S.G.M. / A snapshot of the emerging tomato genome sequence. In: The Plant Genome. 2009 ; Vol. 2, No. 1. pp. 78-92.
@article{ba48e8fdebb84e429b1e564b2af9ae9f,
title = "A snapshot of the emerging tomato genome sequence",
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",
author = "L.A. Mueller and {Klein Lankhorst}, R.M. and S.D. Tanksley and R.M. Peters and {van Staveren}, M.J. and E. Datema and M.W.E.J. Fiers and {van Ham}, R.C.H.J. and D. Szinay and {de Jong}, J.H.S.G.M.",
year = "2009",
doi = "10.3835/plantgenome2008.08.0005",
language = "English",
volume = "2",
pages = "78--92",
journal = "The Plant Genome",
issn = "1940-3372",
publisher = "Crop Science Society of America",
number = "1",

}

Mueller, LA, Klein Lankhorst, RM, Tanksley, SD, Peters, RM, van Staveren, MJ, Datema, E, Fiers, MWEJ, van Ham, RCHJ, Szinay, D & de Jong, JHSGM 2009, 'A snapshot of the emerging tomato genome sequence', The Plant Genome, vol. 2, no. 1, pp. 78-92. https://doi.org/10.3835/plantgenome2008.08.0005

A snapshot of the emerging tomato genome sequence. / Mueller, L.A.; Klein Lankhorst, R.M.; Tanksley, S.D.; Peters, R.M.; van Staveren, M.J.; Datema, E.; Fiers, M.W.E.J.; van Ham, R.C.H.J.; Szinay, D.; de Jong, J.H.S.G.M.

In: The Plant Genome, Vol. 2, No. 1, 2009, p. 78-92.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - A snapshot of the emerging tomato genome sequence

AU - Mueller, L.A.

AU - Klein Lankhorst, R.M.

AU - Tanksley, S.D.

AU - Peters, R.M.

AU - van Staveren, M.J.

AU - Datema, E.

AU - Fiers, M.W.E.J.

AU - van Ham, R.C.H.J.

AU - Szinay, D.

AU - de Jong, J.H.S.G.M.

PY - 2009

Y1 - 2009

N2 - 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

AB - 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

U2 - 10.3835/plantgenome2008.08.0005

DO - 10.3835/plantgenome2008.08.0005

M3 - Article

VL - 2

SP - 78

EP - 92

JO - The Plant Genome

JF - The Plant Genome

SN - 1940-3372

IS - 1

ER -

Mueller LA, Klein Lankhorst RM, Tanksley SD, Peters RM, van Staveren MJ, Datema E et al. A snapshot of the emerging tomato genome sequence. The Plant Genome. 2009;2(1):78-92. https://doi.org/10.3835/plantgenome2008.08.0005