Solanum burkartii PG4005 Assembly & Annotation

Overview

Analysis Name Solanum burkartii PG4005 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 1,212,308,977 bp
Contig number 3158
Contig N50 5,388,693 bp
Contig L50 44
Contig longest 39,069,489 bp
Assembly level Contig

Assembly

The Solanum burkartii PG4005 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) PG4005.fa.gz

Gene Predictions

The Solanum burkartii PG4005 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PG4005.gff.gz
CDS sequences (FASTA file) PG4005.cds.fa.gz
Protein sequences (FASTA file) PG4005.protein.fa.gz

Functional Analysis

Functional annotation for the Solanum burkartii PG4005 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_burkartii_PG4005.Pfam.tsv.gz

S genes

Summary

QueryContigSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF10Ψatg001770206085604-84376Solanum chilense KJ814888.1, SLF1092.6-
SLF19atg0050501658477114-478229Solanum tuberosum DM8.1, SLF1995.7F-box domain
SLF21atg0077113798593284-94504Solanum tuberosum DM8.1, SLF2196.2F-box domain
SLF20atg00771137985478972-480138Solanum tuberosum DM8.1, SLF2096.7F-box domain
SLF7atg00771137985495071-496240Solanum tuberosum DM8.1, SLF797.4F-box domain
SLF5atg00771137985534773-535942Solanum tuberosum DM8.1, SLF5-298.4F-box domain
SLF4Ψatg00771137985684923-686078Solanum pimpinellifolium
KJ814871.1, SLF4		94.8-
SLF12atg00771137985828812-827646Solanum tuberosum DM8.1, SLF1299.1F-box domain
SLF5-2atg00771137985846353-847537Solanum tuberosum DM8.1, SLF597.2F-box domain
SLF18atg019890883718546-17434Solanum tuberosum DM8.1, SLF1895.7F-box domain
SLF11Ψatg0317853005845006-846176Solanum tuberosum DM8.1, SLF1196.2-
SLF9Ψatg0386850239633947-632804Solanum tuberosum DM8.1, SLF997.6-
SLF15atg0619201148101238-99979Solanum tuberosum DM8.1, SLF1597.4F-box domain
SLF18-2Ψatg0996448929015-10133Solanum tuberosum DM8.1, SLF1895.8-
S-RNase-1atg1996260368309-8545,
8633-9046		Solanum tuberosum
XM_006347185.1, RNase1		97.5Ribonuclease T2 family
S-RNase-2hptg001832810532580906-2581142,
2581230-2581643		Solanum tuberosum
XM_006347185.1, RNase1		97.5Ribonuclease T2 family
SLF22hptg001832810533014776-3015927Solanum tuberosum DM8.1, SLF22-295.9F-box domain
SLF6hptg004368996853790-52645Solanum tuberosum DM8.1, SLF694.4F-box domain
SLF17hptg0043689968653041-651860Solanum tuberosum DM8.1, SLF1797.5F-box domain
S-RNase-3hptg00695605962238691-238921,
239032-239445		Solanum tuberosum
MZ561411.1, SRNase-S8		93.6Ribonuclease T2 family
SLF10-2Ψhptg00695605962776187-774960Solanum chilense
KJ814888.1, SLF10		90.4-
SLF23hptg006956059621140112-1141269Solanum lycopersicoides
KU960925.1, SLF23		96.0F-box domain
SLF17-2hptg006956059621171437-1172618Solanum tuberosum DM8.1, SLF1796.9-
SLF4-2Ψhptg006956059622164559-2165727Solanum pimpinellifolium
KJ814871.1, SLF4		95.5F-box domain
SLF12-2hptg006956059622325433-2324267Solanum tuberosum DM8.1, SLF1298.3F-box domain
SLF5-3hptg006956059622407052-2408236Solanum tuberosum DM8.1, SLF597.0F-box domain
SLF5-4hptg006956059622685376-2686545Solanum tuberosum DM8.1, SLF5-298.5F-box domain
SLF7-2hptg006956059622706795-2705626Solanum tuberosum DM8.1, SLF797.5F-box domain
SLF20-2hptg006956059622717865-2716699Solanum tuberosum DM8.1, SLF2096.6F-box domain
SLF21-2hptg006956059623096897-3095677Solanum tuberosum DM8.1, SLF2196.3F-box domain
SLF9-2Ψhptg006956059624770649-4769521Solanum tuberosum DM8.1, SLF996.0-
SLF13hptg0122339057189279-190481Solanum tuberosum DM8.1, SLF1398.3F-box domain
SLF12-3Ψhptg0155307103849549-48401Solanum pennellii
NM_001323464.1, SLF12		92.9-
SLF11-2Ψhptg015530710382170009-2171179Solanum tuberosum DM8.1, SLF1196.1-
SLF1Ψhptg018614236711199132-1200313Solanum peruvianum
KJ814846.1, SLF1		92.3-
SLF1-2Ψhptg0244200768104268-103091Solanum pennellii
KJ814858.1, SLF1		91.2-
SLF16Ψptg003166862142907666-2908846Solanum tuberosum DM8.1, SLF1698.0-
SLF15-2ptg003166862144690285-4689026Solanum tuberosum DM8.1, SLF1597.4F-box domain
SLF19-2ptg004391370446203907-6205022Solanum tuberosum DM8.1, SLF1995.6F-box domain
SLF18-3ptg004391370446227459-6226347Solanum tuberosum DM8.1, SLF1895.4F-box domain
SLF12-4Ψptg006412297908941953-943102Solanum pennellii
NM_001323464.1, SLF12		93.1-
SLF13-2ptg0064122979081530756-1529554Solanum tuberosum DM8.1, SLF1398.2F-box domain

Nucleotide

Protein

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