Solanum boliviense PG5076 Assembly & Annotation

Overview

Analysis Name Solanum boliviense PG5076 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 1,517,385,590 bp
Contig number 3193
Contig N50 2,456,379 bp
Contig L50 112
Contig longest 35,908,915 bp
Assembly level Contig

Assembly

The Solanum boliviense PG5076 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) PG5076.fa.gz

Gene Predictions

The Solanum boliviense PG5076 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PG5076.gff.gz
CDS sequences (FASTA file) PG5076.cds.fa.gz
Protein sequences (FASTA file) PG5076.protein.fa.gz

Functional Analysis

Functional annotation for the Solanum boliviense PG5076 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_boliviense_PG5076.Pfam.tsv.gz

S genes

Summary

QueryContigSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF9atg0186744958593920-595062Solanum tuberosum DM8.1, SLF998.7F-box domain
SLF13atg019247044951268177-1266975Solanum tuberosum DM8.1, SLF1398.8F-box domain
SLF18atg02769483697370-6252Solanum tuberosum DM8.1, SLF1898.1F-box domain
SLF22atg0300727765464307-465446Solanum tuberosum DM8.1, SLF2298.4F-box domain
SLF16atg03092267436757496-758676Solanum tuberosum DM8.1, SLF1699F-box domain
SLF11atg04621574548873322-872204Solanum tuberosum DM8.1, SLF1192.5F-box domain
SLF15atg0632744151212615-211356Solanum tuberosum DM8.1, SLF1597.5F-box domain
SLF19atg09565877633973-32861Solanum tuberosum DM8.1, SLF1995.1F-box domain
SLF12ψatg16192253015384-14238Solanum tuberosum DM8.1, SLF1296.2-
SLF17hptg000753850921372243-1371062Solanum tuberosum DM8.1, SLF1797.5F-box domain
SLF23hptg000753850921375501-1374341Solanum lycopersicoides
KU960925.1, SLF23		94.8F-box domain
SLF5hptg000753850923978666-3977485Solanum tuberosum DM8.1, SLF595.1F-box domain
SLF12-2ψhptg000753850923987378-3988521Solanum tuberosum DM8.1, SLF1296.4-
SLF5-2hptg000753850924241572-4240403Solanum tuberosum DM8.1, SLF5-297.5F-box domain
SLF7hptg000753850924333943-4332774Solanum tuberosum DM8.1, SLF797.1F-box domain
SLF6ψhptg000753850924365559-4364421Solanum tuberosum DM8.1, SLF692.6-
SLF20hptg000753850924413447-4412281Solanum tuberosum DM8.1, SLF2098.8F-box domain
SLF21hptg000753850924893196-4891973Solanum tuberosum DM8.1, SLF2197.8F-box domain
SLF5-3hptg00862085067170465-169275Solanum tuberosum DM8.1, SLF595.6F-box domain
SLF12-3ψhptg00862085067175964-177129Solanum tuberosum DM8.1, SLF1297-
SLF17-2hptg00862085067230383-229202Solanum tuberosum DM8.1, SLF1797.4F-box domain
SLF23-2hptg00862085067252613-251456Solanum neorickii
MG266239.1, SLF23		95.4F-box domain
SLF13-2ptg004993373777300549-7301751Solanum tuberosum DM8.1, SLF1399.2F-box domain
SLF11-2ψptg004993373778636476-8635364Solanum tuberosum DM8.1, SLF1196.5-
SLF15-2ψptg00753715618526020-524764Solanum tuberosum DM8.1, SLF1597.7-
SLF16-2ptg007537156182529114-2527934Solanum tuberosum DM8.1, SLF1699.1F-box domain
SLF19-2ptg00821683849412955649-12956761Solanum tuberosum DM8.1, SLF1995.1F-box domain
SLF18-2ptg00821683849412989868-12988750Solanum tuberosum DM8.1, SLF1898.3F-box domain
SLF22-2ψptg01021048459769265-770404Solanum tuberosum DM8.1, SLF2298.5-
S-RNaseptg0106476325427947-28189,
28303-28728		Solanum tuberosum
MZ561410.1, SRNase-S7		99.4Ribonuclease T2 family
SLF4ptg01064763254475793-474630Solanum pimpinellifolium
KJ814871.1, SLF4		94.9F-box domain
SLF5-4ptg01064763254585518-584349Solanum tuberosum DM8.1, SLF5-298.6F-box domain
SLF7-2ptg01064763254635269-634100Solanum tuberosum DM8.1, SLF797.7F-box domain
SLF6-2ψptg01064763254670107-668969Solanum tuberosum DM8.1, SLF692.3-
SLF20-2ptg01064763254717998-716832Solanum tuberosum DM8.1, SLF2098.7F-box domain
SLF21-2ptg011735563211499548-1498325Solanum tuberosum DM8.1, SLF2197.7F-box domain
SLF9-2ptg011735563212794220-2793078Solanum tuberosum DM8.1, SLF998.7F-box domain

Nucleotide

Protein

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