Solanum sogarandinum PG4032 Assembly & Annotation

Overview

Analysis Name Solanum sogarandinum PG4032 Assembly & Annotation
Sequencing technology PacBio data and Hi-C data
Assembly method hifiasm (v.0.13)
Release Date 2022-06-08
Reference Publication(s)

Tang D, Jia Y, Zhang J, Li H, Cheng L, Wang P, Bao Z, Liu Z, Feng S, Zhu X, Li D, Zhu G, Wang H, Zhou Y, Zhou Y, Bryan GJ, Buell CR, Zhang C, Huang S. Genome evolution and diversity of wild and cultivated potatoes. Nature. 2022 Jun;606(7914):535-541. doi: 10.1038/s41586-022-04822-x.

Abstract

Potato (Solanum tuberosum L.) is the world’s most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We fnd that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the efect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confdence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplifed by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.

Assembly statistics

Contig total length 1,537,782,622 bp
Contig number 3392
Contig N50 8,271,425 bp
Contig L50 36
Contig longest 59,618,472 bp
Assembly level Contig

Assembly

The Solanum sogarandinum PG4032 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) PG4032.fa.gz

Gene Predictions

The Solanum sogarandinum PG4032 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PG4032.gff.gz
CDS sequences (FASTA file) PG4032.cds.fa.gz
Protein sequences (FASTA file) PG4032.protein.fa.gz

Functional Analysis

Functional annotation for the Solanum sogarandinum PG4032 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_sogarandinum_PG4032.Pfam.tsv.gz

S genes

Summary

QueryContigSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF11Ψatg00291009984578920-577755Solanum tuberosum DM8.1, SLF1195.1 -
SLF16Ψatg01064002564378015-376827Solanum tuberosum DM8.1, SLF1698.2 F-box domain
SLF13atg02171091949116814-118016Solanum tuberosum DM8.1, SLF1396.7 F-box domain
SLF12Ψatg02171091949407599-406438Solanum chilense KJ814890.1, SLF1292.3 -
SLF15atg09886668132036-33295Solanum tuberosum DM8.1, SLF1598.1 F-box domain
S-RNasehptg00272807169748306-748524,
748629-749057
Solanum peruvianum
AB072467.1, SpS25-RNase
94.0 Ribonuclease T2 family
SLF21hptg002728071691748893-1750116Solanum tuberosum DM8.1, SLF2191.4 F-box domain
SLF6hptg002728071692212322-2213461Solanum tuberosum DM8.1, SLF6-295.6 F-box domain
SLF1hptg00585042497330149-328968Solanum pennellii KJ814858.1, SLF192.1 F-box domain
SLF23hptg00585042497700946-702115Solanum lycopersicoides
KU960925.1, SLF23
95.1 F-box domain
SLF17hptg00585042497766868-768049Solanum tuberosum DM8.1, SLF1798.1 F-box domain
SLF20hptg0066684579555984-557150Solanum tuberosum DM8.1, SLF2096.7 F-box domain
SLF6-2hptg0066684579609173-610282Solanum tuberosum DM8.1, SLF690.8F-box domain
SLF7hptg0066684579622907-624070Solanum tuberosum DM8.1, SLF795.4 F-box domain
SLF9hptg00702528229869879-871021Solanum tuberosum DM8.1, SLF997.2 F-box domain
SLF5hptg0073557742320987-319791Solanum tuberosum DM8.1, SLF596.0 F-box domain
SLF12-2hptg0073557742331912-333081Solanum tuberosum DM8.1, SLF1297.4 F-box domain
SLF4Ψhptg0073557742346672-345506Solanum pimpinellifolium
KJ814871.1, SLF4
94.7 -
SLF5-2hptg0073557742489108-487939Solanum tuberosum DM8.1, SLF5-296.5 F-box domain
SLF19ptg00015457461329227404-29228516Solanum tuberosum DM8.1, SLF1995.5 F-box domain
SLF18ptg00015457461329284559-29283441Solanum tuberosum DM8.1, SLF1897.3 F-box domain
SLF13-2ptg00015457461341791352-41792554Solanum tuberosum DM8.1, SLF1396.7 F-box domain
SLF12-3Ψptg00015457461342083115-42081954Solanum chilense KJ814890.1, SLF1292.3 -
SLF17-2ptg00015457461343170856-43169696Solanum tuberosum DM8.1, SLF1797.5 F-box domain
SLF6-3ptg00015457461343420042-43421184Solanum tuberosum DM8.1, SLF693.2 F-box domain
S-RNase-2ptg00015457461343811423-43811656,
43811743-43812156
Solanum tuberosum
MZ561415.1, SRNase-S12
94.5 Ribonuclease T2 family
SLF5-3ptg00015457461351508233-51507049Solanum tuberosum DM8.1, SLF597.5 F-box domain
SLF12-4ptg00015457461351509552-51510718Solanum tuberosum DM8.1, SLF1297.8 F-box domain
SLF5-4ptg00015457461351949419-51948250Solanum tuberosum DM8.1, SLF5-297.6 F-box domain
SLF7-2ptg00015457461352341431-52340265Solanum tuberosum DM8.1, SLF795.0 F-box domain
SLF20-2ptg00015457461352452072-52450906Solanum tuberosum DM8.1, SLF2098.5 F-box domain
SLF21-2ptg00015457461352739296-52738076Solanum tuberosum DM8.1, SLF2197.0 F-box domain
SLF9-2ptg00015457461353714590-53713448Solanum tuberosum DM8.1, SLF997.6 F-box domain
SLF16-2ptg00402989460525481878-25483092Solanum tuberosum DM8.1, SLF1698.2 F-box domain
SLF15-2ptg00402989460526691922-26693181Solanum tuberosum DM8.1, SLF1598.1 F-box domain
SLF11-2Ψptg00471033983564190-563025Solanum tuberosum DM8.1, SLF1195.1 -

Nucleotide

Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences