| Analysis Name | Solanum galapagense gwh_assembly LA0317 Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | hifiasm v1.0 |
| Release Date | 2022-06-21 |
Yu X, Qu M, Shi Y, Hao C, Guo S, Fei Z, Gao L. Chromosome-scale genome assemblies of wild tomato relatives Solanum habrochaites and Solanum galapagense reveal structural variants associated with stress tolerance and terpene biosynthesis. Hortic Res. 2022 Jun 20;9:uhac139. doi: 10.1093/hr/uhac139.
Assembly statistics
| Genome size (bp) | 859,928,289 |
| GC content | 34.82% |
| Genome sequence No. | 1,116 |
| Maximum genome sequence length (bp) | 96,570,058 |
| Minimum genome sequence length (bp) | 18,337 |
| Average genome sequence length (bp) | 770,545 |
| Genome sequence N50 (bp) | 68,406,545 |
| Genome sequence N90 (bp) | 52,401,859 |
| Assembly level | Chromosome |
The Solanum galapagense gwh_assembly LA0317 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHBJTJ00000000.genome.fasta.gz |
The Solanum galapagense gwh_assembly LA0317 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GWHBJTJ00000000.gff.gz |
| CDS sequences (FASTA file) | GWHBJTJ00000000.CDS.fasta.gz |
| Protein sequences (FASTA file) | GWHBJTJ00000000.Protein.faa.gz |
Functional annotation for the Solanum galapagense gwh_assembly LA0317 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_galapagense_gwh.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF15 | Chr1 | 96570058 | 2178022-2176763 | Solanum lycopersicum SL2.31, SLF15 | 99.7 | F-box domain |
| SLF16 | Chr1 | 96570058 | 2739342-2738161 | Solanum lycopersicum SL2.31, SLF16 | 99.7 | F-box domain |
| SLF17Ψ | Chr1 | 96570058 | 47210579-47211664 | Solanum lycopersicum SL2.31, SLF17 | 99.5 | - |
| SLF1Ψ | Chr1 | 96570058 | 49356798-49357967 | Solanum lycopersicum NM_001301439.2, SLF1 | 99.3 | - |
| S-RNase | Chr1 | 96570058 | 50162676-50162437,50162339-50161914 | Solanum galapagense OK091157.1, SRNase | 96.7 | Ribonuclease T2 family |
| SLF2Ψ | Chr1 | 96570058 | 51151099-51149918 | Solanum pimpinellifolium KJ814870.1, SLF2 | 99.7 | - |
| SLF12Ψ | Chr1 | 96570058 | 51207541-51208672 | Solanum lycopersicum SL2.31, SLF12 | 99.6 | - |
| SLF4Ψ | Chr1 | 96570058 | 51274842-51273676 | Solanum lycopersicum KJ814943.1, SLF4 | 99.2 | - |
| SLF5Ψ | Chr1 | 96570058 | 51355607-51354439 | Solanum pimpinellifolium KJ814872.1, SLF5 | 100 | - |
| SLF6 | Chr1 | 96570058 | 51373102-51371957 | Solanum lycopersicum KJ814944.1, SLF6 | 99.8 | F-box domain |
| SLF8Ψ | Chr1 | 96570058 | 51932363-51931194 | Solanum lycopersicum SL2.31, SLF8 | 99.7 | - |
| SLF7Ψ | Chr1 | 96570058 | 51957102-51956005 | Solanum lycopersicum SL2.31, SLF7 | 100 | - |
| SLF9 | Chr1 | 96570058 | 54159120-54158056 | Solanum lycopersicum NM_001329461.2, SLF9 | 99.6 | F-box domain |
| SLF10Ψ | Chr1 | 96570058 | 54595530-54596761 | Solanum lycopersicum KJ814899.1, SLF10 | 99.8 | - |
| SLF11 | Chr1 | 96570058 | 56563798-56564970 | Solanum pimpinellifolium KJ814877.1, SLF11 | 100 | F-box domain |
| SLF12-2 | Chr1 | 96570058 | 58362328-58361165 | Solanum lycopersicum NM_001301441.1, SLF12 | 99.7 | F-box domain |
| SLF13 | Chr1 | 96570058 | 59215935-59214742 | Solanum lycopersicum NM_001301435.1, SLF13 | 99.9 | F-box domain |
| SLF14Ψ | Chr1 | 96570058 | 62653581-62652411 | Solanum lycopersicum KJ814903.1, SLF14 | 100 | - |
| SLF18 | Chr1 | 96570058 | 73985914-73987029 | Solanum lycopersicum SL2.31, SLF18 | 99.8 | F-box domain |
| SLF19 | Chr1 | 96570058 | 74004951-74003842 | Solanum lycopersicum SL2.31, SLF19 | 99.7 | F-box domain |
Nucleotide
Protein