Solanum brevicaule PG5032 Assembly & Annotation

Overview

Analysis Name Solanum brevicaule PG5032 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 1,506,277,342 bp
Contig number 3566
Contig N50 1,798,416 bp
Contig L50 160
Contig longest 23,586,765 bp
Assembly level Contig

Assembly

The Solanum brevicaule PG5032 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) PG5032.fa.gz

Gene Predictions

The Solanum brevicaule PG5032 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PG5032.gff.gz
CDS sequences (FASTA file) PG5032.cds.fa.gz
Protein sequences (FASTA file) PG5032.protein.fa.gz

Functional Analysis

Functional annotation for the Solanum brevicaule PG5032 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_brevicaule_PG5032.Pfam.tsv.gz

S genes

Summary

QueryContigSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF22Ψatg01401018212133212-134351Solanum tuberosum DM8.1, SLF2298.7-
SLF15atg0184614915281439-282701Solanum tuberosum DM8.1, SLF1597.7F-box domain
SLF19atg0263180895357397-58512Solanum tuberosum DM8.1, SLF1996.9F-box domain
SLF18atg0263180895389186-88071Solanum tuberosum DM8.1, SLF1897.4F-box domain
SLF16Ψatg039823457499618-100798Solanum tuberosum DM8.1, SLF1698.3-
SLF13atg0414953614206470-205268Solanum tuberosum DM8.1, SLF1399.3F-box domain
SLF21atg21102914526372-27586Solanum tuberosum DM8.1, SLF2194.2F-box domain
SLF9hptg01021361660272138-270996Solanum tuberosum DM8.1, SLF997.7F-box domain
SLF20hptg0104169395540226-41392Solanum tuberosum DM8.1, SLF2097.1F-box domain
SLF7hptg01041693955315183-316352Solanum tuberosum DM8.1, SLF794.2F-box domain
SLF5hptg01041693955541873-543042Solanum tuberosum DM8.1, SLF5-297F-box domain
SLF4Ψhptg01041693955623681-624834Solanum pimpinellifolium KJ814871.1, SLF493.5-
SLF12hptg01041693955765647-764481Solanum tuberosum DM8.1, SLF1297.7F-box domain
SLF5-2hptg01041693955778444-779634Solanum tuberosum DM8.1, SLF595.8F-box domain
SLF21-2hptg010416939551374724-1373510Solanum tuberosum DM8.1, SLF2194.2F-box domain
SLF21-3hptg011039568352081-3295Solanum tuberosum DM8.1, SLF2194.2F-box domain
SLF9-2hptg011039568353529225-3528083Solanum tuberosum DM8.1, SLF998.3F-box domain
SLF6Ψhptg023128088732511316-2510174Solanum tuberosum DM8.1, SLF6-297.3-
S-RNasehptg0329649926323232-323011,
322885-322457		Solanum chacoense AF176533.1,
ScS12-RNase		99.5Ribonuclease T2 family
SLF21-4hptg0343392195208887-210105Solanum tuberosum DM8.1, SLF2198.7F-box domain
SLF17hptg0382315662243712-242546Solanum peruvianum KU960916.1, SLF1792F-box domain
SLF23hptg0382315662314210-313053Solanum neorickii MG266233.1, SLF2394.1F-box domain
SLF7-2hptg059114899367071-65899Solanum tuberosum DM8.1, SLF794.1F-box domain
SLF19-2ptg003656473083214461-3215576Solanum tuberosum DM8.1, SLF1997F-box domain
SLF18-2ptg003656473083255196-3254081Solanum tuberosum DM8.1, SLF1897.7F-box domain
SLF6-2Ψptg00599943603906259-905140Solanum tuberosum DM8.1, SLF6-294.6-
SLF13-2ptg005999436031404802-1403600Solanum tuberosum DM8.1, SLF1399.3F-box domain
SLF5-3ptg00701313004165454-166623Solanum tuberosum DM8.1, SLF5-297.1F-box domain
SLF12-2ptg00701313004468101-466935Solanum tuberosum DM8.1, SLF1297.1F-box domain
SLF5-4ptg00701313004477407-478597Solanum tuberosum DM8.1, SLF596F-box domain
SLF17-2ptg00701313004983767-982601Solanum peruvianum KU960916.1, SLF1791.6F-box domain
SLF23-2ptg007013130041105050-1103893Solanum neorickii MG266233.1, SLF2394.5F-box domain
SLF22-2ptg018321718511303086-1301969Solanum tuberosum DM8.1, SLF2296.8F-box domain
SLF15-2ptg01911091159817007-818266Solanum tuberosum DM8.1, SLF1597.7F-box domain
SLF16-2Ψptg0201774258136899-138079Solanum tuberosum DM8.1, SLF1697.6-

Nucleotide

Protein

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