| Analysis Name | Solanum scabrum gwh_assembly PI 643126 01 Assembly & Annotation |
| Sequencing technology | PacBio HiFi |
| Assembly method | Hifiasm v0.16.1-r375 |
| Release Date | 2023-03-21 |
Wu Y, Li D, Hu Y, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, Zhang C, Städler T, Buckler ES, Huang S. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell. 2023 May 25;186(11):2313-2328.e15. doi: 10.1016/j.cell.2023.04.008.
SummaryHybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
Assembly statistics
| Genome size (bp) | 3,006,187,379 |
| GC content | 36.64% |
| Contig sequence No. | 5,331 |
| Maximum contig sequence length (bp) | 8,620,688 |
| Minimum contig sequence length (bp) | 8,433 |
| Average contig sequence length (bp) | 563,907 |
| Contig N50 (bp) | 1,416,492 |
| Contig N90 (bp) | 330,622 |
| Assembly level | Contig |
The Solanum scabrum gwh_assembly PI 643126 01 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHBKCC00000000.genome.fasta.gz |
The Solanum scabrum gwh_assembly PI 643126 01 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GWHBKCC00000000.gff.gz |
| CDS sequences (FASTA file) | GWHBKCC00000000.CDS.fasta.gz |
| Protein sequences (FASTA file) | GWHBKCC00000000.Protein.faa.gz |
Functional annotation for the Solanum scabrum gwh_assembly PI 643126 01 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_scabrum_gwh_PI_643126_01.Pfam.tsv.gz |
Summary
| Query | Contig | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF18 | GWHBKCC00000122 | 742059 | 656892-658010 | Solanum tuberosum DM8.1, SLF18 | 87.9 | F-box domain |
| SLF19 | GWHBKCC00000122 | 742059 | 699859-698759 | Solanum tuberosum DM8.1, SLF19 | 90.8 | F-box domain |
| SLF21Ψ | GWHBKCC00000125 | 1696573 | 1229261-1230474 | Solanum tuberosum DM8.1, SLF21 | 87.0 | - |
| SLF22Ψ | GWHBKCC00000383 | 2312416 | 142223-141087 | Solanum tuberosum DM8.1, SLF22 | 86.7 | - |
| SLF11 | GWHBKCC00000488 | 3285942 | 744293-745462 | Solanum tuberosum DM8.1, SLF11 | 88.9 | F-box domain |
| SLF | GWHBKCC00000490 | 2906607 | 2803694-2804851 | Solanum chilense KF475783.1, SLF-ZF5-1 | 87.2 | F-box domain |
| SLF21-2Ψ | GWHBKCC00000800 | 949349 | 9441-10654 | Solanum tuberosum DM8.1, SLF21 | 86.8 | - |
| SLF5 | GWHBKCC00000976 | 664347 | 223554-222385 | Solanum tuberosum DM8.1, SLF5-2 | 87.2 | F-box domain |
| SLF7 | GWHBKCC00001039 | 4482429 | 3067016-3068185 | Solanum tuberosum DM8.1, SLF7 | 88.2 | F-box domain |
| SLF16Ψ | GWHBKCC00001053 | 257340 | 199317-200505 | Solanum tuberosum DM8.1, SLF16 | 87.6 | - |
| SLF19-2 | GWHBKCC00001063 | 551132 | 27372-28469 | Solanum tuberosum DM8.1, SLF19 | 88.6 | F-box domain |
| SLF19-3 | GWHBKCC00001063 | 551132 | 72181-73278 | Solanum tuberosum DM8.1, SLF19 | 88.6 | F-box domain |
| SLF19-4 | GWHBKCC00001063 | 551132 | 116975-118072 | Solanum tuberosum DM8.1, SLF19 | 88.6 | F-box domain |
| SLF19-5 | GWHBKCC00001063 | 551132 | 157539-158636 | Solanum tuberosum DM8.1, SLF19 | 88.5 | F-box domain |
| SLF18-2 | GWHBKCC00001063 | 551132 | 204141-203026 | Solanum lycopersicum SL2.31, SLF18 | 88.5 | F-box domain |
| SLF22-2Ψ | GWHBKCC00001340 | 980973 | 343348-342212 | Solanum tuberosum DM8.1, SLF22 | 87.3 | - |
| SLF19-6Ψ | GWHBKCC00001432 | 479621 | 30966-29887 | Solanum tuberosum DM8.1, SLF19 | 88.6 | - |
| SLF15Ψ | GWHBKCC00001636 | 1250407 | 51886-53145 | Solanum tuberosum DM8.1, SLF15 | 90.3 | - |
| SLF16-2Ψ | GWHBKCC00001636 | 1250407 | 639089-637906 | Solanum tuberosum DM8.1, SLF16 | 88.4 | - |
| SLF19-7Ψ | GWHBKCC00001712 | 1025684 | 54219-55320 | Solanum tuberosum DM8.1, SLF19 | 90.2 | - |
| SLF18-3 | GWHBKCC00001712 | 1025684 | 101373-100264 | Solanum tuberosum DM8.1, SLF18 | 88.8 | F-box domain |
| SLF11-2 | GWHBKCC00002054 | 1127140 | 673008-671839 | Solanum tuberosum DM8.1, SLF11 | 89.3 | F-box domain |
| SLF22-3Ψ | GWHBKCC00002084 | 1268471 | 1119745-1120880 | Solanum tuberosum DM8.1, SLF22 | 87.1 | - |
| SLF19-8 | GWHBKCC00002284 | 590647 | 8144-7047 | Solanum tuberosum DM8.1, SLF19 | 88.6 | F-box domain |
| SLF19-9 | GWHBKCC00002284 | 590647 | 57021-55924 | Solanum tuberosum DM8.1, SLF19 | 88.6 | F-box domain |
| SLF19-10 | GWHBKCC00002284 | 590647 | 158436-157339 | Solanum tuberosum DM8.1, SLF19 | 88.0 | F-box domain |
| SLF15-2 | GWHBKCC00002430 | 913695 | 268218-269477 | Solanum tuberosum DM8.1, SLF15 | 90.2 | F-box domain |
| SLF15-3 | GWHBKCC00002703 | 91833 | 55844-54585 | Solanum tuberosum DM8.1, SLF15 | 90.3 | F-box domain |
| SLF16-3 | GWHBKCC00002711 | 751851 | 625331-624147 | Solanum tuberosum DM8.1, SLF16 | 88.0 | F-box domain |
Nucleotide
Protein