agReg-SNPdb Plants






Georg-August-Universität Göttingen
CiBreed

Overview for Solanum lycopersicum (Tomato)

The tomato (Solanum lycopersicum ) belongs to the nightshade family (Solanaceae) and is thus closely related to other edible plants such as the potato, the bell pepper or the eggplant. The tomato originates from the Andean region in South America and was brought to Europe in the 16th century. Its current genome assembly is ~828 Mb in size and contains 12 chromosomes. In agReg-SNPdb, we store 33,869 genes and 60,973,560 SNPs.


tomato


Statistics

(Last updated on 08.02.2022)

Number of chromosomes 12
Number of genes 33,869
Number of SNPs 60,973,560

Click on a chromosome to download the data stored in agReg-SNPdb for the complete chromosome

Chromosome Number of SNPs Number of Genes
1 7,561,534 4,252
10 5,153,625 2,549
11 4,125,678 2,323
12 5,151,384 2,436
2 3,910,850 3,417
3 5,116,674 3,356
4 5,373,687 2,750
5 5,237,700 2,519
6 3,655,916 2,824
7 5,273,464 2,496
8 4,969,288 2,454
9 5,443,760 2,493



Distribution of rSNPs relative to the TSS

SNP distance to TSS tomato
Distribution of SNPs around the TSS of tomato. The upper plot shows the counts for the whole promoter region (-7.5 kb to +2.5 kb) in 500 bp intervals. The enlargement shows the proximal promoter region (-750 bp to +250 bp) in 50 bp intervals. The red asterisk annotates the position of the TSS.


Input data (Ensembl Plants)

Plant Assembly version Download links
Solanum lycopersicum (tomato) SL3.0 Reference genome
SNPs
Genes
(downloaded on 22 December 2021)