Genome

Solanum lycopersicum (tomato) Solanum lycopersicum Organism overview Lineage: Eukaryota[13895]; Viridiplantae[1517]; Streptophyta[1408]; Embryophyta[1399]; Tracheophyta[1381]; Spermatophyta[1364]; Magnoliopsida[1339]; eudicotyledons[1083]; Gunneridae[1083]; Pentapetalae[1083]; asterids[331]; lamiids[215]; Solanales[85]; Solanaceae[76]; Solanoideae[61]; Solaneae[53]; Solanum[52]; Solanum subgen. Lycopersicon[12]; Solanum lycopersicum[1]

Solanum lycopersicum has been used for a number of firsts in molecular genetics of plants. The use of RFLP (restriction fragment length polymorphism) to generate a linkage map of a complete plant genome was done with tomato (Bernatzky and Tanksley. Genetics 1986; 112:887-898). Tomato was the organism where quantitative traits were resolved into More...Mendelian factors (Paterson et al.). The use of allelic variation of RAPD (random amplification of polymorphic DNA) to facilitate map-based walking to agronomically pertinent loci was first done in tomato (Wing et al. and Martin et al.). The creation of a high-density molecular linkage map and the use for comparative genomics were done with tomato and potato (Tanksley et al.). In February 2011 the chromosome pseudomolecules were deposited in NCBI. Less...

Summary Sequence data:  genome assemblies: 27; sequence reads: 163  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 792.735  median protein count: 37604  median GC%: 34.4976 NCBI Annotation Release:  103 Publications (limited to 20 most recent records) De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum  lycopersicum var. cerasiforme, by long-read sequencing. Takei H, et al. DNA Res 2021 Jan 19 A high-continuity and annotated tomato reference genome. Su X, et al. BMC Genomics 2021 Dec 15 Linkage between the I-3 gene for resistance to Fusarium wilt race 3 and increased sensitivity to bacterial spot in tomato. Li J, et al. Theor Appl Genet 2018 Jan An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato. Yamaguchi H, et al. Theor Appl Genet 2018 Jun Genome-Wide Study of the Tomato SlMLO Gene Family and Its Functional Characterization in Response to the Powdery Mildew Fungus Oidium neolycopersici. Zheng Z, et al. Front Plant Sci 2016 Roles and regulation of cytokinins in tomato fruit development. Matsuo S, et al. J Exp Bot 2012 Sep Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. Aoki K, et al. BMC Genomics 2010 Mar 30 Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Wang Y, et al. Theor Appl Genet 2005 Dec A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Budiman MA, et al. Genome Res 2000 Jan More...  Representative (genome information for reference and representative genomes) Reference genome:   Solanum lycopersicum SL3.1 Submitter: Solanaceae Genomics Project Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr 1 NC_015438.3 CM001064.3 98.46 35.6 4,790 12 89 1,172 3,898 197 Chr 2 NC_015439.3 CM001065.3 55.98 35.8 3,997 - 65 1,276 3,017 80 Chr 3 NC_015440.3 CM001066.3 72.29 36.4 3,820 2 70 743 3,019 87 Chr 4 NC_015441.3 CM001067.3 66.56 35.2 3,124 - 66 654 2,586 102 Chr 5 NC_015442.3 CM001068.3 66.72 35.2 2,437 2 54 559 2,142 111 Chr 6 NC_015443.3 CM001069.3 49.79 35.9 3,302 3 97 588 2,667 86 Chr 7 NC_015444.3 CM001070.3 68.18 35.5 2,745 - 36 584 2,324 78 Chr 8 NC_015445.3 CM001071.3 65.99 35.5 2,737 - 59 578 2,233 74 Chr 9 NC_015446.3 CM001072.3 72.91 35.8 2,630 - 40 600 2,201 79 Chr 10 NC_015447.3 CM001073.3 65.63 34.8 2,520 - 77 483 2,298 122 Chr 11 NC_015448.3 CM001074.3 56.6 35.8 2,526 12 37 444 2,038 105 Chr 12 NC_015449.3 CM001075.3 68.13 35.7 2,537 - 56 679 2,200 99 - NC_007898.3 - 0.16 37.9 87 8 45 - 142 2 - NC_035963.1 - 0.45 45.1 39 5 27 - 72 2 Un - . - 20.14 39.3 313 7 10 73 382 36 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources AGI C.M. Rick Tomato Genetics Resource Center GOLD Genomic and Biotechnology of the fruits Kazusa DNA Research Institute National Research Centre on Plant Biotechnology - India