| Analysis Name | Solanum commersonii CM1.0 Assembly & Annotation |
| Sequencing technology | PacBio HiFi, Oxford Nanopore, Illumina Hi-C |
| Assembly method | - |
| Release Date | 2024-05-25 |
Feng Y, Zhou J, Li D, Wang Z, Peng C, Zhu G. The haplotype-resolved T2T genome assembly of the wild potato species Solanum commersonii provides molecular insights into its freezing tolerance. Plant Commun. 2024 May 27:100980. doi: 10.1016/j.xplc.2024.100980.
SummaryIn summary, we generated the first haplotype-resolved T2T potato genome assembly (CM1.0), which captured all centromeres and 47 telomeres. The genome of S. commersonii provided us with the opportunity to characterize the genome structure and anti-freezing traits. Comparative transcriptome indicated that The MAP kinases and ROS scavenging system contributed its freezing tolerance. This study provides invaluable resources for functional genomics and will further facilitate genetic improvement of potato.
Assembly statistics
| The total size of Hap1 | 707.40 Mb |
| The total size of Hap2 | 712.10 Mb |
| Contig N50 of Hap1 | 48.90 Mb |
| Contig N50 of Hap2 | 55.24 Mb |
| Assembly level | Chromosome |
The Solanum commersonii CM1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHESPT00000000.genome.fasta.gz |
The Solanum commersonii CM1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GWHESPT00000000.gff.gz |
| CDS sequences (FASTA file) | GWHESPT00000000.RNA.fasta.gz |
| Protein sequences (FASTA file) | GWHESPT00000000.Protein.faa.gz |
Functional annotation for the Solanum commersonii CM1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_commersonii_CM1.0.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| Hap1_SLF15 | GWHESPT00000001 | 89804714 | 4110716-4109457 | Solanum tuberosum DM8.1, SLF15 | 97.9 | F-box domain |
| Hap1_SLF16 | GWHESPT00000001 | 89804714 | 5360453-5359239 | Solanum tuberosum DM8.1, SLF16 | 97.6 | F-box domain |
| Hap1_SLF17 | GWHESPT00000001 | 89804714 | 33174354-33173173 | Solanum tuberosum DM8.1, SLF17 | 97.2 | F-box domain |
| Hap1_SLF23 | GWHESPT00000001 | 89804714 | 33187532-33186387 | Solanum lycopersicoides KU960925.1, SLF23 | 95.1 | F-box domain |
| Hap1_SLF5 | GWHESPT00000001 | 89804714 | 37260285-37259101 | Solanum tuberosum DM8.1, SLF5 | 97.6 | F-box domain |
| Hap1_SLF12 | GWHESPT00000001 | 89804714 | 37277110-37278276 | Solanum tuberosum DM8.1, SLF12 | 98.6 | F-box domain |
| Hap1_SLF5-2 | GWHESPT00000001 | 89804714 | 37437339-37436170 | Solanum tuberosum DM8.1, SLF5-2 | 98.6 | F-box domain |
| Hap1_SLF7 | GWHESPT00000001 | 89804714 | 37491844-37490675 | Solanum tuberosum DM8.1, SLF7 | 97.9 | F-box domain |
| Hap1_SLF20 | GWHESPT00000001 | 89804714 | 37594917-37593751 | Solanum tuberosum DM8.1, SLF20 | 99.3 | F-box domain |
| Hap1_SLF21 | GWHESPT00000001 | 89804714 | 38077718-38076498 | Solanum tuberosum DM8.1, SLF21 | 98.6 | F-box domain |
| Hap1_SLF3Ψ | GWHESPT00000001 | 89804714 | 44917765-44918915 | Solanum pennellii BK009230.1, SLF3 | 91.7 | - |
| Hap1_SLF13 | GWHESPT00000001 | 89804714 | 45437857-45436661 | Solanum tuberosum DM8.1, SLF13 | 98.0 | F-box domain |
| Hap1_SLF18 | GWHESPT00000001 | 89804714 | 59935414-59936529 | Solanum tuberosum DM8.1, SLF18 | 97.1 | F-box domain |
| Hap1_SLF19Ψ | GWHESPT00000001 | 89804714 | 59977320-59976210 | Solanum tuberosum DM8.1, SLF19 | 95.9 | - |
| Hap1_S-RNase | GWHESPT00000001 | 89804714 | 36399610-36399864,36399969-36400397 | Solanum chacoense CAA40216.1, S2-protein | 80.5 | Ribonuclease T2 family |
| Hap2_SLF15 | GWHESPT00000013 | 93708594 | 3891103-3889844 | Solanum tuberosum DM8.1, SLF15 | 97.9 | F-box domain |
| Hap2_SLF16 | GWHESPT00000013 | 93708594 | 5909247-5908033 | Solanum tuberosum DM8.1, SLF16 | 97.6 | F-box domain |
| Hap2_SLF9 | GWHESPT00000013 | 93708594 | 37002326-37003468 | Solanum tuberosum DM8.1, SLF9 | 98.0 | F-box domain |
| Hap2_SLF21Ψ | GWHESPT00000013 | 93708594 | 38248906-38247688 | Solanum tuberosum DM8.1, SLF21 | 97.1 | - |
| Hap2_SLF5 | GWHESPT00000013 | 93708594 | 39954424-39955593 | Petunia axillaris AB568416.1, S19-SLF5 | 81.3 | F-box domain |
| Hap2_SLF7Ψ | GWHESPT00000013 | 93708594 | 42848156-42849216 | Solanum tuberosum DM8.1, SLF7 | 93.5 | - |
| Hap2_SLF5-2 | GWHESPT00000013 | 93708594 | 43202738-43203907 | Solanum tuberosum DM8.1, SLF5-2 | 96.6 | F-box domain |
| Hap2_SLF4Ψ | GWHESPT00000013 | 93708594 | 43350548-43351689 | Solanum pimpinellifolium KJ814871.1, SLF4 | 94.4 | - |
| Hap2_SLF12 | GWHESPT00000013 | 93708594 | 43420026-43418860 | Solanum tuberosum DM8.1, SLF12 | 97.3 | F-box domain |
| Hap2_SLF5-3 | GWHESPT00000013 | 93708594 | 43428818-43430008 | Solanum tuberosum DM8.1, SLF5 | 96.2 | F-box domain |
| Hap2_SLF17 | GWHESPT00000013 | 93708594 | 45276602-45275421 | Solanum tuberosum DM8.1, SLF17 | 97.2 | F-box domain |
| Hap2_SLF23 | GWHESPT00000013 | 93708594 | 45316753-45315605 | Solanum neorickii MG266239.1, SLF23 | 94.8 | F-box domain |
| Hap2_SLF1Ψ | GWHESPT00000013 | 93708594 | 45413562-45414702 | Solanum peruvianum KJ814846.1, SLF1 | 90.0 | - |
| Hap2_SLF11Ψ | GWHESPT00000013 | 93708594 | 45925337-45926438 | Solanum tuberosum DM8.1, SLF11 | 93.2 | - |
| Hap2_SLF6 | GWHESPT00000013 | 93708594 | 47757043-47755892 | Solanum tuberosum DM8.1, SLF6-2 | 96.5 | F-box domain |
| Hap2_SLF3Ψ | GWHESPT00000013 | 93708594 | 47799814-47800950 | Solanum pennellii BK009230.1, SLF3 | 90.5 | - |
| Hap2_SLF13 | GWHESPT00000013 | 93708594 | 48288406-48287204 | Solanum tuberosum DM8.1, SLF13 | 98.2 | F-box domain |
| Hap2_SLF18 | GWHESPT00000013 | 93708594 | 63110582-63111697 | Solanum tuberosum DM8.1, SLF18 | 97.5 | F-box domain |
| Hap2_SLF19Ψ | GWHESPT00000013 | 93708594 | 63149146-63148036 | Solanum tuberosum DM8.1, SLF19 | 95.9 | - |
| Hap2_S-RNase | GWHESPT00000013 | 93708594 | 40499737-40499483,40499342-40498914 | Solanum tuberosum QYF06679.1, S-RNase 5 | 71.6 | Ribonuclease T2 family |
Nucleotide
Protein