| Analysis Name | Solanum chmielewskii 'ZY60 (cultivar)' ASM2770478v1 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 | 769.4 Mb |
| Number of scaffolds | 329 |
| Scaffold N50 | 61.8 Mb |
| Scaffold L50 | 6 |
| Number of contigs | 823 |
| Contig N50 | 2 Mb |
| Contig L50 | 117 |
| Assembly level | Scaffold |
The Solanum chmielewskii 'ZY60 (cultivar)' ASM2770478v1 assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | S.chmielewskii.genomic.fa.gz |
The Solanum chmielewskii 'ZY60 (cultivar)' ASM2770478v1 genome gene prediction files are available in FASTA format.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | S.chmielewskii.cds.fa.gz |
| Protein sequences (FASTA file) | S.chmielewskii.pep.fa.gz |
Functional annotation for the Solanum chmielewskii 'ZY60 (cultivar)' ASM2770478v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_chmielewskii_ZY60_ASM2770478v1.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF15 | Chr01 | 89956309 | 1540821-1539568 | Solanum lycopersicum SL2.31, SLF15 | 97.9 | F-box domain |
| SLF16 | Chr01 | 89956309 | 1852554-1851373 | Solanum lycopersicum SL2.31, SLF16 | 99.4 | F-box domain |
| SLF22Ψ | Chr01 | 89956309 | 41546241-41545107 | Solanum peruvianum KU987616.1, SLF22 | 99.3 | - |
| SLF9 | Chr01 | 89956309 | 44070893-44072035 | Solanum pimpinellifolium KJ814875.1, SLF9 | 98.6 | F-box domain |
| SLF20 | Chr01 | 89956309 | 45487210-45488376 | Solanum peruvianum KU960913.1, SLF20 | 98 | F-box domain |
| SLF6 | Chr01 | 89956309 | 46229641-46230786 | Solanum peruvianum KJ814850.1, SLF6 | 98.7 | F-box domain |
| SLF5 | Chr01 | 89956309 | 46278081-46279250 | Solanum habrochaites KJ814915.1, SLF5-S1 | 96.1 | F-box domain |
| SLF4 | Chr01 | 89956309 | 46358780-46359946 | Solanum pimpinellifolium KJ814871.1 SLF4 | 96.6 | F-box domain |
| SLF2Ψ | Chr01 | 89956309 | 46493419-46494445 | Solanum peruvianum KJ814847.1, SLF2 | 97.9 | - |
| S-RNase | Chr01 | 89956309 | 47927568-47927813,47927928-47928353 | Solanum peruvianum Z26581.1, Sn-RNase | 96.7 | Ribonuclease T2 family |
| SLF23 | Chr01 | 89956309 | 49327980-49329137 | Solanum chmielewskii MG266249.1, SLF23 | 99.9 | F-box domain |
| SLF17Ψ | Chr01 | 89956309 | 49565208-49566388 | Solanum peruvianum KU987615.1, SLF17 | 96.1 | - |
| SLF1 | Chr01 | 89956309 | 49914448-49915623 | Solanum pennellii KJ814858.1, SLF1 | 91.8 | F-box domain |
| SLF11 | Chr01 | 89956309 | 50559343-50560515 | Solanum lycopersicoides KU987623.1, SLF11 | 99.7 | F-box domain |
| SLF12 | Chr01 | 89956309 | 51561523-51560360 | Solanum lycopersicoides KU987622.1, SLF12 | 98.9 | F-box domain |
| SLF13Ψ | Chr01 | 89956309 | 52272953-52271751 | Solanum peruvianum KJ814856.1, SLF13 | 98.8 | - |
| SLF14Ψ | Chr01 | 89956309 | 55634981-55633812 | Solanum lycopersicum KJ814903.1, SLF14 | 98.5 | - |
| SLF18 | Chr01 | 89956309 | 67098384-67099499 | Solanum lycopersicum SL2.31, SLF18 | 99.1 | F-box domain |
| SLF19 | Chr01 | 89956309 | 67116638-67115529 | Solanum lycopersicum SL2.31, SLF19 | 98.9 | F-box domain |
Nucleotide
Protein