| Analysis Name | Solanum habrochaites gwh_assembly LA0407 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 habrochaites 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) | 950,673,181 |
| GC content | 34.97% |
| Genome sequence No. | 1,009 |
| Maximum genome sequence length (bp) | 109,540,374 |
| Minimum genome sequence length (bp) | 3,000 |
| Average genome sequence length (bp) | 942,193 |
| Genome sequence N50 (bp) | 72,063,167 |
| Genome sequence N90 (bp) | 58,730,508 |
| Assembly level | Chromosome |
The Solanum habrochaites gwh_assembly LA0407 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHBJTH00000000.genome.fasta.gz |
The Solanum habrochaites gwh_assembly LA0407 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GWHBJTH00000000.gff.gz |
| CDS sequences (FASTA file) | GWHBJTH00000000.CDS.fasta.gz |
| Protein sequences (FASTA file) | GWHBJTH00000000.Protein.faa.gz |
Functional annotation for the Solanum habrochaites gwh_assembly LA0407 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_habrochaites_gwh.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF15 | Chr1 | 109540374 | 2541084-2539825 | Solanum lycopersicum SL2.31, SLF15 | 96.9 | F-box domain |
| SLF16 | Chr1 | 109540374 | 3228673-3227492 | Solanum lycopersicum SL2.31, SLF16 | 99 | F-box domain |
| SLF1 | Chr1 | 109540374 | 54780499-54779330 | Solanum peruvianum KJ814846.1, SLF1 | 95.6 | F-box domain |
| SLF17 | Chr1 | 109540374 | 55055308-55056474 | Solanum peruvianum KU960916.1, SLF17 | 99.1 | F-box domain |
| SLF14 | Chr1 | 109540374 | 55870429-55869260 | Solanum pennellii BK009220.1, SLF14 | 98 | F-box domain |
| SLF4 | Chr1 | 109540374 | 56052192-56051320 | Solanum pimpinellifolium KJ814871.1, SLF4 | 96.5 | F-box domain |
| SLF23 | Chr1 | 109540374 | 56062526-56063683 | Solanum pennellii BK009221.1, SLF23 | 99.1 | F-box domain |
| S-RNase | Chr1 | 109540374 | 57225365-5722559557225688-57226101 | Solanum habrochaites AB072478.1, Sh_hgSRN1 | 85.6 | Ribonuclease T2 family |
| SLF2 | Chr1 | 109540374 | 59138023-59136842 | Solanum habrochaites KJ814908.1, SLF2-S1 | 98.1 | F-box domain |
| SLF4-2 | Chr1 | 109540374 | 59282492-59281326 | Solanum pimpinellifolium KJ814871.1, SLF4 | 96.7 | F-box domain |
| SLF7 | Chr1 | 109540374 | 59718811-59717642 | Solanum habrochaites KJ814923.1, SLF7-S1 | 98.7 | F-box domain |
| SLF20 | Chr1 | 109540374 | 59845664-59844498 | Solanum peruvianum KU960913.1, SLF20 | 98.1 | F-box domain |
| SLF10Ψ | Chr1 | 109540374 | 60312759-60313988 | Solanum pimpinellifolium KJ814876.1, SLF10 | 97.7 | - |
| SLF9 | Chr1 | 109540374 | 60547814-60548956 | Solanum pimpinellifolium KJ814875.1, SLF9 | 98.3 | F-box domain |
| SLF21 | Chr1 | 109540374 | 61601909-61603207 | Solanum peruvianum KU960914.1, SLF21 | 98.6 | F-box domain |
| SLF11 | Chr1 | 109540374 | 63693780-63694952 | Solanum pimpinellifolium KJ814877.1, SLF11 | 98.6 | F-box domain |
| SLF17-2 | Chr1 | 109540374 | 64293419-64292238 | Solanum lycopersicoides KU960921.1, SLF17 | 96.3 | F-box domain |
| SLF14-2Ψ | Chr1 | 109540374 | 72512834-72514004 | Solanum lycopersicum KJ814903.1, SLF14 | 98.5 | - |
| SLF13 | Chr1 | 109540374 | 76128658-76129644 | Solanum habrochaites KJ814930.1, SLF13 | 99.2 | F-box domain |
| SLF12 | Chr1 | 109540374 | 76688997-76687834 | Solanum habrochaites KJ814929.1, SLF12 | 99.5 | F-box domain |
| SLF18 | Chr1 | 109540374 | 84792432-84793547 | Solanum lycopersicum SL2.31, SLF18 | 98 | F-box domain |
| SLF19 | Chr1 | 109540374 | 84811087-84809978 | Solanum tuberosum DM8.1, SLF19 | 92.6 | F-box domain |
Nucleotide
Protein