Kazusa Tomato Genomics Database

KaTomicsDB is a portal website for the tomato genomics databases for DNA markers, SNP annotations, and genome sequences released from our research group. Refer to Shirasawa and Hirakawa (2013).

Tomato Marker DataBase

DNA markers, e.g., SNP and SSR, and genetic linkage maps in tomato

Tomato Functional SNP DataBase

SNP annotations based on the predicted genes in the tomato genome

Tomato SBM DataBase

Genome sequences for gene-rich regions within the tomato genome

Tomato organelle genome assembly and genes

Gene annotation files (gff, cds, and pep) for CMS tomato lines [ Kuwabara et al. 2021 bioRxiv ]

KDRItomato2020MPF2.vcf.gz (454 KB)

This VCF (Variant Call Format) file includes 965 SNP sites from an F2 population derived from a cross between P110 and M110. [ Safaei et al. 2020 Plant Genome ]

KDRItomatoMTvsREG2016.vcf (19 MB)

This VCF (Variant Call Format) file includes 1,187,941 SNP sites from whole-genome resequencing data for Micro-Tom and Regina. [ Shirasawa et al. 2016 DNA Res ]

KDRItomatoRAD4enzymes2016.vcf (603 KB)

This VCF (Variant Call Format) file includes 29,702 SNP sites from ddRAD-Seq data (EcoRI/HindIII, PstI/MspI, PstI/EcoRI, and SalI/PstI) for Micro-Tom and Regina. [ Shirasawa et al. 2016 DNA Res ]

KDRItomatoRAD6cultivars2016.vcf (917 KB)

This VCF (Variant Call Format) file includes 41,909 SNP sites from ddRAD-Seq data (PstI/MspI) for 6 cultivars. [ Shirasawa et al. 2016 DNA Res ]

KDRItomatoRMF2.ref.mct (11 KB)

This MCT (MapChart Format) file includes 1,257 SNP loci on a genetic map based on the tomato genome sequence, SL2.50. [ Shirasawa et al. 2016 DNA Res ]

KDRItomatoRMF2.denovo.mct (10 KB)

This MCT (MapChart Format) file includes 686 SNP loci on a genetic map based on a de novo assembly of RAD reads. [ Shirasawa et al. 2016 DNA Res ]

KDRItomatoMutants2016.vcf (271 KB)

This VCF (Variant Call Format) file includes 5,145 mutations of 4 EMS and 3 gamma-ray Micro-Tom mutants. [ Shirasawa et al. 2016 Plant Biotechnol J ]

KDRItomatoMicro-Tom2016.vcf (44 MB)

This VCF (Variant Call Format) file includes 1,140,687 spontaneous SNPs in Micro-Tom lines. [ Shirasawa et al. 2016 Plant Biotechnol J ]

KDRItomatoSNP2013.hmp.txt (229 KB)

This HapMap file includes 1,247 SNPs genotyped with the Illumina GoldenGate array across 663 accessions. [ Shirasawa et al. 2013 DNA Research 20: 593-603 ]

KDRItomatoSNP2013.vcf (11 MB)

This VCF (Variant Call Format) file includes 1,473,798 SNP sites from resequencing data for 6 accessions. [ Shirasawa et al. 2013 DNA Research 20: 593-603 ]

Portal Sites

PGDBj http://pgdbj.jp/
SGN http://solgenomics.net/
Plants Database http://plants.usda.gov/java/profile?symbol=SOLY2
PURDUE University http://www.hort.purdue.edu/rhodcv/hort410/tomat/tomat.htm
SGR http://solanaceae.plantbiology.msu.edu/

Genome databases

PlantGDB http://www.plantgdb.org/SlGDB/
TOMATOMICS http://bioinf.mind.meiji.ac.jp/tomatomics/
Tomato SBM Database http://www.kazusa.or.jp/tomato_sbm/

DNA marker databases

Marker DB http://marker.kazusa.or.jp/tomato/
VegMarks http://vegmarks.nivot.affrc.go.jp/VegMarks/jsp/
PIP Database http://ibi.zju.edu.cn/pgl/pip/download.html
SolCAP http://solcap.msu.edu/
dbSNP http://www.ncbi.nlm.nih.gov/snp/?term=Solanum+lycopersicum&SITE=NcbiHome&submit=Go
Tomato SNP http://www-plb.ucdavis.edu/labs/maloof/tomatosnp/
gabiPD http://www.gabipd.org/projects/Pomamo/

EST databases

MiBASE http://www.kazusa.or.jp/jsol/microtom/
KafTom http://www.pgb.kazusa.or.jp/kaftom/
TrichOME http://www.planttrichome.org/trichomedb/estbyspecies_detail.jsp?species=Solanum%20lycopersicum

Gene expression databases

TomPLEX http://www.plexdb.org/plex.php?database=Tomato
SGED http://www.jcvi.org/potato/
Functional Genomics DB http://ted.bti.cornell.edu/
DATFAP http://cgi-www.daimi.au.dk/cgi-chili/datfap/frontdoor.py
PlantTFDB http://planttfdb.cbi.pku.edu.cn/index.php?sp=Sly

Metabolome databases

KaPPA-View4 http://kpv.kazusa.or.jp/
MassBase http://webs2.kazusa.or.jp/massbase/

Plant material databases

BreeDB https://www.eu-sol.wur.nl/
ECPGR http://documents.plant.wur.nl/cgn/pgr/tomato/
TGRC http://tgrc.ucdavis.edu/
TOMATOMA http://tomatoma.nbrp.jp/index.jsp
Tomato mutagenesis http://zamir.sgn.cornell.edu/mutants/
LycoTILL http://www.agrobios.it/tilling/

Others

Functional SNP DB http://plant1.kazusa.or.jp/tomato/
GMDD http://gmdd.shgmo.org/event/view/113
Solanaceae Source http://www.nhm.ac.uk/research-curation/research/projects/solanaceaesource/
TGC http://tgc.ifas.ufl.edu/

Contact

2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 JAPAN

F markerdb at kazusa.or.jp