| Analysis Name | Solanum pennellii SPENNV200 Assembly & Annotation |
| Sequencing technology | Illumina(paired-end, mate-pair sequencing), BAC library |
| Assembly method | - |
| Release Date | 2014-7-11 |
Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet. 2014 Sep;46(9):1034-8. doi: 10.1038/ng.3046.
AbstractSolanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
Assembly statistics
| Genome size | 926.4 Mb |
| Number of chromosomes | 12 |
| Number of scaffolds | 12 |
| Scaffold N50 | 78 Mb |
| Scaffold L50 | 6 |
| Number of contigs | 30,753 |
| Contig N50 | 60.1 kb |
| Contig L50 | 4,136 |
| Assembly level | Chromosome |
The Solanum pennellii SPENNV200 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_001406875.2_SPENNV200_genomic.fna.gz |
The Solanum pennellii SPENNV200 genome gene prediction files are not available.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | - |
| Protein sequences (FASTA file) | - |
Functional annotation for the Solanum pennellii SPENNV200 is not available.
Downloads
| Domain from InterProScan | - |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF15 | HG975440.1 | 109333515 | 2463138-2461879 | Solanum lycopersicum SL2.31, SLF15 | 97.2 | F-box domain |
| SLF16 | HG975440.1 | 109333515 | 3048388-3047207 | Solanum lycopersicum SL2.31, SLF16 | 98.7 | F-box domain |
| SLF22 | HG975440.1 | 109333515 | 55310065-55311198 | Solanum pennellii BK009218.1, SLF22 | 100.0 | F-box domain |
| SLF17 | HG975440.1 | 109333515 | 57343380-57344561 | Solanum pennellii BK009219.1, SLF17 | 100.0 | F-box domain |
| SLF14 | HG975440.1 | 109333515 | 57575058-57573889 | Solanum pennellii BK009220.1, SLF14 | 100.0 | F-box domain |
| SLF23 | HG975440.1 | 109333515 | 57730925-57732082 | Solanum pennellii BK009221.1, SLF23 | 100.0 | F-box domain |
| SLF13 | HG975440.1 | 109333515 | 59555089-59553908 | Solanum pennellii BK009222.1, SLF13 | 100.0 | F-box domain |
| SLF11 | HG975440.1 | 109333515 | 59677718-59676552 | Solanum pennellii BK009223.1, SLF11 | 100.0 | F-box domain |
| SLF10 | HG975440.1 | 109333515 | 59763510-59762341 | Solanum pennellii BK009224.1, SLF10 | 100.0 | F-box domain |
| SLF6Ψ | HG975440.1 | 109333515 | 59780871-59779727 | Solanum pennellii KJ814862.1, SLF6 | 99.7 | - |
| SLF8 | HG975440.1 | 109333515 | 60199761-60198592 | Solanum pennellii BK009225.1, SLF8 | 100.0 | F-box domain |
| SLF20 | HG975440.1 | 109333515 | 60360766-60359600 | Solanum pennellii BK009226.1, SLF20 | 100.0 | F-box domain |
| SLF21 | HG975440.1 | 109333515 | 60586390-60585089 | Solanum pennellii BK009227.1, SLF21 | 100.0 | F-box domain |
| SLF6-2 | HG975440.1 | 109333515 | 61822489-61821347 | Solanum pennellii BK009228.1, SLF6 | 100.0 | F-box domain |
| SLF10-2Ψ | HG975440.1 | 109333515 | 62275923-62277089 | Solanum pennellii KJ814865.1, SLF10 | 99.8 | - |
| SLF4 | HG975440.1 | 109333515 | 63408490-63409662 | Solanum pennellii BK009229.1, SLF4 | 100.0 | F-box domain |
| SLF3 | HG975440.1 | 109333515 | 65226205-65225042 | Solanum pennellii BK009230.1, SLF3 | 100.0 | F-box domain |
| SLF2 | HG975440.1 | 109333515 | 65999303-65998116 | Solanum pennellii BK009231.1, SLF2 | 100.0 | F-box domain |
| SLF14-2Ψ | HG975440.1 | 109333515 | 70121818-70120636 | Solanum chilense KJ814892.1, SLF14 | 97.0 | - |
| SLF18 | HG975440.1 | 109333515 | 85165871-85166986 | Solanum lycopersicum SL2.31, SLF18 | 97.8 | F-box domain |
| SLF19 | HG975440.1 | 109333515 | 85196800-85195691 | Solanum lycopersicum SL2.31, SLF19 | 97.9 | F-box domain |
Nucleotide
Protein