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International Tomato Genome Sequencing Project

  • The tomato genome was published in Nature on 2012, work by the Tomato Genome Consortium, a multi-national team of scientists from 14 countries including Korea.
  • All data (tomato genome and annotation) is openly and freely available on SGN, MIPS, and Genbank.
  • Genome browser for exploring the tomato reference genome (ITAG 2.3) is available from in TGsol.

[Contributor 1] Resequencing projects ; prof. Kang, Hankyong National University

  • The Resequencing data from tomato genome of four domestic cultivars were provided by prof. Kang in Hankyong National University.
  • SNP detected in these resequencing data were used to build SNP marker database for molecular marker development.

[Contributor 2] Genetic resources Collection ; prof. Park, Pusan National University

  • Prof. Parks team have been collect and multiply elite lines of genetic resources sequenced the genome. In addition, the team secured about 75 accessions of tomato germplasm and conducted phenotyping.

Resource Data infomation

Reference genome (ITAG2.3)

Crops Scientific name Genome size Chromosome number Total length(bp) Gene Loci Final
Tomato S. Lycopersicum Heinz 1706-BG 950 Mb 12 718,969,627 34,727 chromosome

NCBI-SRA Resequencing Data

Species name No. of SRA No. of SRA used for analysis
Solanum lycopersicum 557 126
Solanum lycopersicum var. cerasiforme 133 126
Solanum pimpinellifolium 65 33
Solanum habrochaites 17 1
Solanum pennellii 14 0
Solanum arcanum 12 0
Solanum huaylasense 3 0
Solanum cheesmaniae 2 2
Solanum chilense 2 1
Solanum chmielewskii 2 0
Etc. (Solanum neorickii, peruvianum, corneliomuelleri, galapagense) 6 3
Total 813 234
< * ~June 2016 >

NCBI-SRA Transcriptome Data

Experiment Title Instrument Library Total lenth(bp)
Solanum lycopersicum PI114490 SE RNA-Seq Illumina Genome Analyzer IIx RNA-Seq 1,809,075,540
Solanum lycopersicum T5 SE RNA-Seq Illumina Genome Analyzer IIx RNA-Seq 1,708,971,720
Solanum lycopersicum OH9242 SE RNA-Seq Illumina Genome Analyzer IIx RNA-Seq 1,353,093,900
Solanum lycopersicum NC84173 SE RNA-Seq Illumina Genome Analyzer IIx RNA-Seq 1,383,236,700
Solanum lycopersicum FL7600 SE RNA-Seq Illumina Genome Analyzer IIx RNA-Seq 1,702,107,120
Solanum pimpinellifolium PI212816 SE2 RNA-Seq Illumina Genome Analyzer IIx RNA-Seq 1,554,019,740
Solanum pimpinellifolium PI212816 SE1 RNA-Seq Illumina Genome Analyzer IIx RNA-Seq 921,292,920
Solanum lycopersicum trasncriptome sequencing of unpollinated style (M82) 454 GS FLX EST 39,349,666
< * ~June 2016 >

Resequencing data of four Domestic cultivar Resequencing Data

Sample No. of Read Average length per read (bp) Total length (bp) Genome coverage
K1 72,683,850 90.31 8.40x 66,637,536 (91.68%)
K2 75,345,050 91.15 8.79x 68,002,695 (90.26%)
K3 78,327,298 90.79 9.10x 74,696,500 (95.36%)
K4 76,705,424 90.47 8.88x 70,719,624 (92.20%)

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