- The Tomato Integrated Database -

Data obtained from our project

Micro-Tom information


Full-length cDNA

Expression sequence tags

Genomic DNA-seq and natural polymorphism

  • DNA sequencing of Micro-Tom genome (SRA accession nos.: DRX000454, DRX000455 and DRX000482) and variant (SNPs and InDels) call with Heinz 1706 reference genome (version SL2.4) have been performed as reported by Kobayashi and colleagues (2014).
  • Since Heinz 1706 reference genome was updated to SL2.5, variant call between the SL2.5 and Micro-Tom genome were performed using the same DNA-seq data (see Kudo et al. 2017 for details).
  • TOMATOMICS stores infomration on the called variants: 1,692,098 SNPs, 143,518 insertions, and 92,137 deletions.

TMCS version 1.2.1 (July 15, 2016 release)


TMCS v1.2.1 is structural annotations of tomato protein-coding genes on SL2.5 genome (Kudo et al. 2017).

Materials and Methods

  • TMCS v1.2.1 was made by integrating assembly results of RNA-seq reads with cufflinks, mapping results of the HTC sequences, and existing ITAG2.4 annotation.
  • SRA accession numbers of RNA-seq data used in this study were SRR404309-SRR404322 and SRR404324-SRR404324.
  • The RNA-seq reads were mapped onto SL2.5 genome with a Bowtie2-TopHat2 pipline and then assembled with the cufflinks software.
  • Annotation (GFF) files of ITAG2.4 and HTCs were merged using the cuffmerge program, and then used as a supervisor in the RNA-seq assembly
  • Prediction of open reading frames (ORFs) were performed using TransDecoder software.
  • The ORF prediction was supervised by a blastp similartity search result agianst TAIR10 protein database and by a hmmscan domain search result against PfamA database.

Statistics [PDF]

Stats Locus Transcript Exon Intron CDS 5'-UTR 3'-UTR
Number 28,796 54,783 - - 54,783 38,228 41,657
Length: mean (bp) 5,466 1,435 256 816 1,257 268 434
Length: minimum (bp) 297 63 1 10 297 1 1
Length: 1st quantile (bp) 1,374 575 83 102 648 70 209
Length: median (bp) 3,021 1,209 134 244 1,014 142 300
Length: 3rd quantile (bp) 6,065 1,923 281 770 1,581 271 461
Length: maximum (bp) 294,264 219,418 23,288 283,525 15,315 20,902 18,866

Data obtained from public databases

Genomic sequence


Genomic annotations


  • ITAG2.4 genomic annotations including gene models, non-coding RNA, and repeats were obtained from the SGN database.

SGN unigenes


  • Information on unigenes was obtained from the SGN database.

Expression sequence tags


  • EST sequences (solanum_lycopersicum_mRNA_2008_10_21.seq) were obtained from the SGN database (FTP site).

T-DNA tagging


  • Sixty nine T-DNA flanking sequences of Micro-Tom mutants were obtained from the TOMATOMA database (Saito et al. 2011, Shikata et al. 2016).
  • Of the 68 sequences, 62 were mapped onto the SL2.5 genome.
  • TOMATOMICS stores information on T-DNA insertion sites predicted by the mapping.

RNA-seq (Heinz 1706)


  • These RNA-seq reads were mapped onto SL2.5 genome with a Bowtie2-TopHat2 pipline (browsable on a JBrowse page).
  • The mapping results were used to construct TMCS v1.2.1.
Organ/tissue/stage SRA accession numbers
Leaves SRR404309, SRR404310
Roots SRR404311, SRR404312
Flowers SRR404315, SRR404316
Flower buds SRR404315, SRR404316
Fruits, 1 cm immature green SRR404317, SRR404318
Fruits, 2 cm immature green SRR404319, SRR404320
Fruits, 3 cm immature green SRR404321, SRR404322
Fruits, mature green SRR404324, SRR404325
Fruits, breaker SRR404326, SRR404327
Fruits, 10 days after breaker SRR404328, SRR404329

RNA-seq (Micro-Tom)


  • These RNA-seq reads were mapped onto SL2.5 genome with a Bowtie2-TopHat2 pipline (browsable on a JBrowse page).
Organ/tissue/stage SRA accession numbers
Flower buds, 2 days before anthesis SRR988278, SRR988418, SRR988529
Flowers at anthesis SRR988530, SRR988531, SRR988532
Flowers, 4 days after anthesis SRR988533, SRR988534, SRR988535

'TOMATOMICS' has been developed and maintained by Bioinformatics Laboratory of Meiji University. Last Modified Jul. 31, 2017.