| Analysis Name | Solanum lycopersicoides 'ZY64 (cultivar)' ASM2770504v1 Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | Canu v. 1.5 |
| Release Date | 2023-01-11 |
Li N, He Q, Wang J, Wang B, Zhao J, Huang S, Yang T, Tang Y, Yang S, Aisimutuola P, Xu R, Hu J, Jia C, Ma K, Li Z, Jiang F, Gao J, Lan H, Zhou Y, Zhang X, Huang S, Fei Z, Wang H, Li H, Yu Q. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat Genet. 2023 May;55(5):852-860. doi: 10.1038/s41588-023-01340-y.
AbstractEffective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.
Assembly statistics
| Genome size | 1.2 Gb |
| Number of scaffolds | 1,175 |
| Scaffold N50 | 91.1 Mb |
| Scaffold L50 | 6 |
| Number of contigs | 3,965 |
| Contig N50 | 579 kb |
| Contig L50 | 513 |
| Assembly level | Scaffold |
The Solanum lycopersicoides 'ZY64 (cultivar)' ASM2770504v1 assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_027705045.1_ASM2770504v1_genomic.fna.gz |
The Solanum lycopersicoides 'ZY64 (cultivar)' ASM2770504v1 genome gene prediction files are available in FASTA format.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | S.lycopersicoides.cds.fa.gz |
| Protein sequences (FASTA file) | S.lycopersicoides.pep.fa.gz |
Functional annotation for the Solanum lycopersicoides 'ZY64 (cultivar)' ASM2770504v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_lycopersicoides_ZY64_ASM2770504v1.Pfam.tsv.gz |
Summary
| Query | Scaffold | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF5 | JAKWJB010000210.1 | 111582 | 23278-22109 | Solanum chilense KJ814884.1, SLF5 | 98.1 | F-box domain |
| SLF6 | JAKWJB010000210.1 | 111582 | 43436-42291 | Solanum lycopersicoides KU987626.1, SLF6 | 98.9 | F-box domain |
| SLF19 | JAKWJB010000250.1 | 85999 | 8033-6924 | Solanum lycopersicum SL2.31, SLF19 | 96.2 | F-box domain |
| SLF10Ψ | JAKWJB010000285.1 | 81506 | 18076-19304 | Solanum chilense KJ814888.1, SLF10 | 94.6 | - |
| SLF3Ψ | JAKWJB010000846.1 | 81992 | 58326-59483 | Solanum pennellii BK009230.1, SLF3 | 97.2 | - |
| SLF11 | JAKWJB010000974.1 | 100705 | 10888-9719 | Solanum peruvianum KJ814846.1, SLF1 | 96.3 | F-box domain |
| SLF15 | JAKWJB010001164.1 | 135971647 | 3419543-3418284 | Solanum lycopersicum SL2.31, SLF15 | 95.6 | F-box domain |
| SLF16 | JAKWJB010001164.1 | 135971647 | 3967616-3966435 | Solanum lycopersicum SL2.31, SLF16 | 96.4 | F-box domain |
| SLF23Ψ | JAKWJB010001164.1 | 135971647 | 58860502-58861658 | Solanum lycopersicoides KU960925.1, SLF23 | 98.9 | - |
| SLF5-2 | JAKWJB010001164.1 | 135971647 | 73849360-73848173 | Solanum lycopersicoides KU987627.2, SLF5 | 97.3 | F-box domain |
| SLF4 | JAKWJB010001164.1 | 135971647 | 73954796-73953630 | Solanum peruvianum KJ814848.1, SLF4 | 97 | F-box domain |
| SLF7Ψ | JAKWJB010001164.1 | 135971647 | 74076071-74074903 | Solanum peruvianum KJ814851.1, SLF7 | 97 | - |
| SLF6-2Ψ | JAKWJB010001164.1 | 135971647 | 74086192-74085087 | Solanum tuberosum DM8.1, SLF6 | 90.2 | - |
| SLF21Ψ | JAKWJB010001164.1 | 135971647 | 74462830-74464140 | Solanum lycopersicoides KU960923.1, SLF21 | 99.4 | - |
| SLF20Ψ | JAKWJB010001164.1 | 135971647 | 74855994-74857158 | Solanum lycopersicoides KU960922.1, SLF20 | 99.7 | - |
| SLF9Ψ | JAKWJB010001164.1 | 135971647 | 75656502-75655360 | Solanum lycopersicoides KU987631.1, SLF9 | 99 | - |
| SLF10-2Ψ | JAKWJB010001164.1 | 135971647 | 79658648-79657418 | Solanum chilense KJ814888.1, SLF10 | 94.3 | - |
| SLF11-2Ψ | JAKWJB010001164.1 | 135971647 | 83210579-83211750 | Solanum pennellii NM_001323461.1, SLF11 | 97.4 | - |
| SLF11-3Ψ | JAKWJB010001164.1 | 135971647 | 83265432-83264262 | Solanum pennellii NM_001323461.1, SLF11 | 97.5 | - |
| SLF3-2Ψ | JAKWJB010001164.1 | 135971647 | 85797952-85799113 | Solanum pennellii BK009230.1, SLF3 | 97.8 | - |
| SLF13 | JAKWJB010001164.1 | 135971647 | 86547536-86546334 | Solanum pennellii NM_001323465.1, SLF13 | 98.2 | F-box domain |
| SLF18Ψ | JAKWJB010001164.1 | 135971647 | 104997980-104999093 | Solanum lycopersicum SL2.31, SLF18 | 95.9 | - |
| SLF19-2Ψ | JAKWJB010001164.1 | 135971647 | 105037649-105036548 | Solanum lycopersicum SL2.31, SLF19 | 94 | - |
Nucleotide
Protein