| Analysis Name | Solanum americanum 'sp2271 (Isolate)' Assembly & Annotation |
| Sequencing technology | PacBio CCS |
| Assembly method | HiFiasm v. 0.13 |
| Release Date | 2023-07-06 |
Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet. 2023 Sep;55(9):1579-1588. doi: 10.1038/s41588-023-01486-9.
AbstractPotato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanum accessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanum immune receptor genes. We further screened for variation in recognition of 315 P. infestans RXLR effectors in 52 S. americanum accessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860 and R04373, that recognize cognate P. infestans RXLR effectors PITG_22825 (AVRamr4), PITG_02860 and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.
Assembly statistics
| Genome size | 1.1 Gb |
| Number of chromosomes | 12 |
| Number of scaffolds | 450 |
| Scaffold N50 | 90.7 Mb |
| Scaffold L50 | 6 |
| Number of contigs | 567 |
| Contig N50 | 51.1 Mb |
| Contig L50 | 8 |
| GC percent | 36.5 |
| Assembly level | Chromosome |
The Solanum americanum 'sp2271 (Isolate)' Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | sp2271.v4.fa.gz |
The Solanum americanum 'sp2271 (Isolate)' genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | sp2271.v4.gff3.gz |
| CDS sequences (FASTA file) | sp2271.v4.cds.fa.gz |
| Protein sequences (FASTA file) | sp2271.v4.pep.fa.gz |
Functional annotation for the Solanum americanum 'sp2271 (Isolate)' is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_americanum_sp2271.Pfam.tsv.gz |
Summary
| Query | Chromosome | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF15 | sp2271chr01 | 113123534 | 3595658-3596917 | Solanum tuberosum DM8.1, SLF15 | 90.2 | F-box domain |
| SLF16ψ | sp2271chr01 | 113123534 | 4323391-4322208 | Solanum tuberosum DM8.1, SLF16 | 87.9 | - |
| SLF4ψ | sp2271chr01 | 113123534 | 35743323-35742136 | Petunia hybrida, S9-SLF4 | 77.5 | - |
| SLF22 | sp2271chr01 | 113123534 | 37174305-37173169 | Solanum tuberosum DM8.1, SLF22 | 87.2 | F-box domain |
| SLF12 | sp2271chr01 | 113123534 | 38378629-38379780 | Solanum tuberosum DM8.1, SLF12 | 83.5 | F-box domain |
| SLF6 | sp2271chr01 | 113123534 | 38800764-38801912 | Solanum tuberosum DM8.1, SLF6-2 | 86.1 | F-box domain |
| SLF5 | sp2271chr01 | 113123534 | 39350885-39349716 | Solanum tuberosum DM8.1, SLF5-2 | 87.6 | F-box domain |
| SLF17 | sp2271chr01 | 113123534 | 40624287-40623109 | Solanum peruvianum KU987615.1, SLF17 | 78.5 | F-box domain |
| SLF23 | sp2271chr01 | 113123534 | 40855863-40854706 | Solanum neorickii MG266239.1, SLF23 | 88.5 | F-box domain |
| SLF20ψ | sp2271chr01 | 113123534 | 50885148-50883982 | Solanum tuberosum DM8.1, SLF20 | 88.9 | - |
| SLF9 | sp2271chr01 | 113123534 | 54517286-54516115 | Solanum tuberosum DM8.1, SLF9 | 82.7 | F-box domain |
| SLF20-2ψ | sp2271chr01 | 113123534 | 54761667-54760501 | Solanum tuberosum DM8.1, SLF20 | 87.7 | - |
| SLF21ψ | sp2271chr01 | 113123534 | 63628010-63629223 | Solanum tuberosum DM8.1, SLF21 | 87.0 | - |
| SLF11 | sp2271chr01 | 113123534 | 65305181-65306350 | Solanum tuberosum DM8.1, SLF11 | 89.4 | F-box domain |
| SLF3 | sp2271chr01 | 113123534 | 66409424-66408261 | Solanum pennellii BK009230.1, SLF3 | 84.0 | F-box domain |
| SLF18 | sp2271chr01 | 113123534 | 82939062-82940177 | Solanum lycopersicum SL2.31, SLF18 | 87.8 | F-box domain |
| SLF19 | sp2271chr01 | 113123534 | 82995686-82994586 | Solanum tuberosum DM8.1, SLF19 | 90.6 | F-box domain |
Nucleotide
Protein