| Analysis Name | Solanum lycopersicum 'Heniz 1706 (cultivar)' ASM2240511v1 Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | CANU v. 3.0 |
| Release Date | 2022-03-04 |
Su X, Wang B, Geng X, Du Y, Yang Q, Liang B, Meng G, Gao Q, Yang W, Zhu Y, Lin T. A high-continuity and annotated tomato reference genome. BMC Genomics. 2021 Dec 15;22(1):898. doi: 10.1186/s12864-021-08212-x.
AbstractBackgroundGenetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. ResultsHere, we assembled an updated reference genome of S. lycopersicum cv. Heniz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato. ConclusionOur results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.
Assembly statistics
| Genome size | 797.2 Mb |
| Number of chromosomes | 12 |
| Number of scaffolds | 82 |
| Scaffold N50 | 66.2 Mb |
| Scaffold L50 | 6 |
| Number of contigs | 892 |
| Contig N50 | 2.2 Mb |
| Contig L50 | 104 |
| Assembly level | Chromosome |
The Solanum lycopersicum 'Heniz 1706 (cultivar)' ASM2240511v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_022405115.1_ASM2240511v1_genomic.fna.gz |
The Solanum lycopersicum 'Heniz 1706 (cultivar)' ASM2240511v1 genome gene prediction files are not available.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | - |
| Protein sequences (FASTA file) | - |
Functional annotation for the Solanum lycopersicum 'Heniz 1706 (cultivar)' ASM2240511v1 is not available.
Downloads
| Domain from InterProScan | - |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF15 | CM039652.1 | 91866112 | 2144101-2142842 | SL2.31ch01:2198500-2196501_SLF15 | 100 | F-box domain |
| SLF16 | CM039652.1 | 91866112 | 2666068-2664887 | SL2.31ch01:2723400-2721301_SLF16 | 100 | F-box domain |
| SLF17Ψ | CM039652.1 | 91866112 | 41862564-41861479 | SL2.31ch01:40853100-40851001_SLF17Ψ | 100 | - |
| SLF1 | CM039652.1 | 91866112 | 44862998-44864167 | NM_001301439.2, SLF1 | 100 | F-box domain |
| S-RNase | CM039652.1 | 91866112 | 45672592-4567235345672255-45671830 | XM_004229015.1,Ribonuclease S-3 | 100 | Ribonuclease T2 family |
| SLF2Ψ | CM039652.1 | 91866112 | 46559497-46558316 | KJ814870.1, SLF2 | 100 | - |
| SLF12Ψ | CM039652.1 | 91866112 | 46616065-46617196 | SL2.31ch01:45516501-45518600_SLF12Ψ | 100 | - |
| SLF4Ψ | CM039652.1 | 91866112 | 46683367-46682201 | KJ814943.1, SLF4 | 100 | - |
| SLF5Ψ | CM039652.1 | 91866112 | 46764066-46762898 | KJ814872.1, SLF5 | 100 | - |
| SLF6Ψ | CM039652.1 | 91866112 | 46781602-46780457 | KJ814944.1, SLF6 | 100 | - |
| SLF8Ψ | CM039652.1 | 91866112 | 47338932-47337764 | SL2.31ch01:46243000-46240701_SLF8Ψ | 100 | - |
| SLF7Ψ | CM039652.1 | 91866112 | 47363711-47362614 | SL2.31ch01:46267800-46265701_SLF7Ψ | 100 | - |
| SLF9 | CM039652.1 | 91866112 | 49531820-49530756 | NM_001329461.2, SLF9 | 100 | F-box domain |
| SLF10Ψ | CM039652.1 | 91866112 | 49977014-49978245 | KJ814899.1, SLF10 | 100 | - |
| SLF11 | CM039652.1 | 91866112 | 51928457-51929629 | KJ814877.1, SLF11 | 100 | F-box associated |
| SLF12 | CM039652.1 | 91866112 | 53687508-53686345 | NM_001301441.1, SLF12 | 100 | F-box associated |
| SLF13 | CM039652.1 | 91866112 | 54533010-54531817 | NM_001301435.1, SLF13 | 100 | F-box associated |
| SLF14Ψ | CM039652.1 | 91866112 | 57743756-57742586 | KJ814903.1, SLF14 | 100 | - |
| SLF18 | CM039652.1 | 91866112 | 68901807-68902922 | SL2.31ch01:67739501-67741500_SLF18 | 100 | F-box domain |
| SLF19 | CM039652.1 | 91866112 | 68920831-68919722 | SL2.31ch01:67757501-67759600_SLF19 | 100 | F-box domain |
Nucleotide
Protein