Solanum lycopersicum Assembly and Gene Annotation

About Solanum lycopersicum

Solanum lycopersicum (tomato) is a member of the nightshade family, Solanaceae, which includes a variety of agricultural crop plants (e.g. potato, pepper, eggplant, and tobacco). The tomato originated in the Andean region of South America, was grown by Aztecs in Mesoamerica, and spread to Europe by early Spanish explorers. Today, hundreds of varieties are grown throughout the world, with the largest producers being China and the United States. In addition to its value as a food, the tomato has served as an important model system for the study of fruit ripening, plant-pathogen interactions, and molecular genetic mapping. The nuclear genome contains 12 chromosomes and is ~950 Mbp in size.


Solanum lycopersicum cv. Heinz 1706 was sequenced and assembled by the International Tomato Genome Sequencing Consortium. Assembly version SL2.40 combines a 22X whole genome shotgun sequence (Roche 454) with Sanger sequence data from BAC-ends, fosmid-ends and Selected BAC Mixture sequences, and additional data from Solexa and SOLiD technologies (total genome coverage 27X). The assembly is deposited into DDBJ/EMBL/GenBank under the accession AEKE00000000.2.


Annotation was carried out by the International Tomato Annotation Group (ITAG) using a combination of evidence-based and ab initio methods.


The variation data for Solanum lycopersicum is from the study of genetic variation by whole-genome sequencing of 84 tomato accessions, including cultivated wild relatives representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon group [2]. In detail, the study expored genetic variation in the tomato clade by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups. The variation data has been submitted to the ENA with accession ERP004618, and has been locus-level accessioned using the transPLANT variation archive.



  1. The tomato genome sequence provides insights into fleshy fruit evolution.
    Tomato Genome Consortium. 2012. Nature. 485:635-641.
  2. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
    Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L et al. 2014. Plant J.. 80:136-148.

Picture credit: David Besa from Sonoma, USA (Flickr) [CC-BY-2.0 (], via Wikimedia Commons.

More information

General information about this species can be found in Wikipedia.



AssemblySL2.50, INSDC Assembly GCA_000188115.2, Oct 2014
Database version94.250
Base Pairs737,636,465
Golden Path Length823,630,941
Genebuild bySolTub_3.0
Genebuild methodImported from ENA
Data sourceSolanaceae Genomics Project

Gene counts

Coding genes33,810
Non coding genes1,382
Small non coding genes1,348
Long non coding genes34
Gene transcripts35,192


Short Variants71,156,260

About this species