Analysis Name | Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 Assembly & Annotation |
Sequencing technology | Illumina HiSeq |
Assembly method | SOAPdenovo v. MAY-2017 |
Release Date | 2021-07-09 |
Yan L, Zhang Y, Cai G, Qing Y, Song J, Wang H, Tan X, Liu C, Yang M, Fang Z, Lai X. Genome assembly of primitive cultivated potato Solanum stenotomum provides insights into potato evolution. G3 (Bethesda). 2021 Sep 27;11(10):jkab262. doi: 10.1093/g3journal/jkab262
AbstractGenetic diversity is the raw material for germplasm enhancement. Landraces and wild species relatives of potato, which contain a rich gene pool of valuable agronomic traits, can provide insights into the genetic diversity behind the adaptability of the common potato. The diploid plant, Solanum stenotomum (Sst), is believed to have an ancestral relationship with modern potato cultivars and be a potential source of resistance against disease. Sequencing of the Sst genome generated an assembly of 852.85 Mb (N50 scaffold size, 3.7 Mb). Pseudomolecule construction anchored 788.75 Mb of the assembly onto 12 pseudochromosomes, with an anchor rate of 92.4%. Genome annotation yielded 41,914 high-confidence protein-coding gene models and comparative analyses with closely related Solanaceae species identified 358 Sst-specific gene families, 885 gene families with expansion along the Sst lineage, and 149 genes experiencing accelerated rates of protein sequence evolution in Sst, the functions of which were mainly associated with defense responses, particularly against bacterial and fungal infection. Insights into the Sst genome and the genomic variation of cultivated potato taxa are valuable in elaborating the impact of potato evolution in early landrace diploid and facilitate modern potato breeding.
Assembly statistics
Genome size | 846.2 Mb |
Number of chromosomes | 12 |
Number of scaffolds | 17,083 |
Scaffold N50 | 62.6 Mb |
Scaffold L50 | 6 |
Number of contigs | 29,155 |
Contig N50 | 127.4 kb |
Contig L50 | 1,679 |
Assembly level | Chromosome |
The Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 Assembly file is available in FASTA format.
Downloads
Chromosomes (FASTA file) | GCF_019186545.1_ASM1918654v1_genomic.fna.gz |
The Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
Genes (GFF3 file) | GCF_019186545.1_ASM1918654v1_genomic.gff.gz |
CDS sequences (FASTA file) | GCF_019186545.1_ASM1918654v1_cds_from_genomic.fna.gz |
Protein sequences (FASTA file) | GCF_019186545.1_ASM1918654v1_protein.faa.gz |
Functional annotation for the Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
Domain from InterProScan | Solanum_stenotomum_F172_ASM1918654v1.Pfam.tsv.gz |
Summary
Query | Chromosome | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
SLF13 | NC_064282.1 | 104650604 | 35349119-35350324 | Solanum tuberosum DM8.1, SLF13 | 98.8 | F-box domain |
SLF11Ψ | NC_064282.1 | 104650604 | 37088682-37087533 | Solanum tuberosum DM8.1, SLF11 | 93.9 | - |
SLF9 | NC_064282.1 | 104650604 | 37939332-37940474 | Solanum tuberosum DM8.1, SLF9 | 98.5 | F-box domain |
SLF21 | NC_064282.1 | 104650604 | 39063296-39064516 | Solanum tuberosum DM8.1, SLF21 | 98.5 | F-box domain |
S-RNase | NC_064282.1 | 104650604 | 39608518-39608291, 39608176-39607745 | Solanum tuberosum MZ561408.1, SRNase-S5 | 88.8 | Ribonuclease T2 family |
SLF5 | NC_064282.1 | 104650604 | 40407843-40406674 | Solanum tuberosum DM8.1, SLF5-2 | 96.0 | F-box domain |
SLF7 | NC_064282.1 | 104650604 | 40517286-40516114 | Solanum tuberosum DM8.1, SLF7 | 93.9 | F-box domain |
SLF12 | NC_064282.1 | 104650604 | 41507598-41506432 | Solanum tuberosum DM8.1, SLF12 | 97.9 | F-box domain |
SLF5-2 | NC_064282.1 | 104650604 | 41517844-41519034 | Solanum tuberosum DM8.1, SLF5 | 95.9 | F-box domain |
SLF5-3Ψ | NC_064282.1 | 104650604 | 42110144-42111326 | Solanum tuberosum DM8.1, SLF5-2 | 95.7 | - |
SLF4Ψ | NC_064282.1 | 104650604 | 42176077-42177241 | Solanum pimpinellifolium KJ814871.1, SLF4 | 94.0 | - |
SLF6Ψ | NC_064282.1 | 104650604 | 42478344-42477205 | Solanum tuberosum DM8.1, SLF6 | 91.8 | - |
SLF19Ψ | NC_064282.1 | 104650604 | 54613659-54614767 | Solanum tuberosum DM8.1, SLF19 | 97.2 | - |
SLF18 | NC_064282.1 | 104650604 | 54662328-54661213 | Solanum tuberosum DM8.1, SLF18 | 97.4 | F-box domain |
SLF22 | NC_064282.1 | 104650604 | 66318649-66317510 | Solanum tuberosum DM8.1, SLF22 | 98.8 | F-box domain |
SLF23 | NC_064282.1 | 104650604 | 67380803-67381960 | Solanum neorickii MG266233.1, SLF23 | 94.4 | F-box domain |
SLF17 | NC_064282.1 | 104650604 | 67452514-67453680 | Solanum tuberosum DM8.1, SLF17 | 98.0 | F-box domain |
SLF16Ψ | NC_064282.1 | 104650604 | 95267648-95268828 | Solanum tuberosum DM8.1, SLF16 | 98.2 | - |
SLF15 | NC_064282.1 | 104650604 | 100652855-100654114 | Solanum tuberosum DM8.1, SLF15 | 97.9 | F-box domain |
Nucleotide
Protein