Solanum buesii PG4041 Assembly & Annotation

Overview

Analysis Name Solanum buesii PG4041 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 1,339,973,848 bp
Contig number 2705
Contig N50 7,998,080 bp
Contig L50 36
Contig longest 44,737,474 bp
Assembly level Contig

Assembly

The Solanum buesii PG4041 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) PG4041.fa.gz

Gene Predictions

The Solanum buesii PG4041 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PG4041.gff.gz
CDS sequences (FASTA file) PG4041.cds.fa.gz
Protein sequences (FASTA file) PG4041.protein.fa.gz

Functional Analysis

Functional annotation for the Solanum buesii PG4041 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_buesii_PG4041.Pfam.tsv.gz

S genes

Summary

QueryContigSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF11Ψatg00311743861247216-246063Solanum tuberosum DM8.1, SLF1197.9-
SLF16atg009117621591485489-1486669Solanum tuberosum DM8.1, SLF1699.3F-box domain
SLF13atg018235430382354841-2356043Solanum tuberosum DM8.1, SLF1399.1F-box domain
SLF6Ψatg018235430382995402-2996548Solanum tuberosum DM8.1, SLF6-297.7-
SLF15atg019014784361322660-1323919Solanum tuberosum DM8.1, SLF1599.8F-box domain
SLF19atg023031841651221360-1222475Solanum tuberosum DM8.1, SLF1997.0F-box domain
SLF18atg023031841651253894-1252779Solanum tuberosum DM8.1, SLF18-297.1F-box domain
SLF18-2atg023031841651262832-1261717Solanum tuberosum DM8.1, SLF1898.1F-box domain
SLF9atg0523133017103135-104277Solanum tuberosum DM8.1, SLF998.9F-box domain
SLF1Ψhptg00062792595608894-607713Solanum pennellii KJ814858.1, SLF190.8-
SLF12hptg00062792595680492-681658Solanum tuberosum DM8.1, SLF1296.6F-box domain
SLF5hptg00062792595819527-818358Solanum tuberosum DM8.1, SLF5-298.5F-box domain
SLF7hptg00062792595885138-883969Solanum tuberosum DM8.1, SLF798.8F-box domain
SLF20hptg00062792595946383-945217Solanum tuberosum DM8.1, SLF2098.5F-box domain
SLF21hptg000627925951405825-1404605Solanum tuberosum DM8.1, SLF2199.3F-box domain
SLF9-2hptg0017938726751772-50630Solanum tuberosum DM8.1, SLF999.2F-box domain
SLF22hptg001793872672004600-2005739Solanum tuberosum DM8.1, SLF2299.4F-box domain
SLF5-2hptg00221764622354211-355395Solanum tuberosum DM8.1, SLF594.4F-box domain
SLF17hptg002217646221415587-1414406Solanum tuberosum DM8.1, SLF1797.5F-box domain
SLF23hptg002217646221441589-1440441Solanum neorickii MG266239.1, SLF2395.0F-box domain
SLF22-2hptg004335799072180760-2179623Solanum tuberosum DM8.1, SLF2299.3F-box domain
SLF12-2hptg0047285857383939-85105Solanum tuberosum DM8.1, SLF1298.1F-box domain
SLF5-3hptg00472858573196634-195465Solanum tuberosum DM8.1, SLF5-298.1F-box domain
SLF7-2hptg00472858573424901-423732Solanum tuberosum DM8.1, SLF796.0F-box domain
SLF20-2hptg00472858573546947-545781Solanum tuberosum DM8.1, SLF2098.1F-box domain
SLF21-2hptg00472858573964469-963249Solanum tuberosum DM8.1, SLF2199.2F-box domain
SLF5-4Ψhptg013417059161033902-1032717Solanum tuberosum DM8.1, SLF596.1-
S-RNasehptg013417059161263000-1262755,
1262642-1262217		Solanum tuberosum MZ561404.1,
S-RNase 1		99.9Ribonuclease T2 family
SLF19-2ptg00174473747429687590-29688705Solanum tuberosum DM8.1, SLF1997.0F-box domain
SLF18-3ptg00174473747429720134-29719019Solanum tuberosum DM8.1, SLF18-296.1F-box domain
SLF18-4ptg00174473747429729067-29727952Solanum tuberosum DM8.1, SLF1898.1F-box domain
SLF13-2ptg00174473747444159843-44161045Solanum tuberosum DM8.1, SLF1399.3F-box domain
SLF6-2Ψptg00174473747444527556-44528683Solanum tuberosum DM8.1, SLF6-296.2-
SLF11-2Ψptg00181826854548367-549520Solanum tuberosum DM8.1, SLF1198.0-
SLF23-2ptg00231916968441005-442153Solanum neorickii MG266239.1, SLF2396.2F-box domain
SLF17-2ptg00231916968473969-475150Solanum tuberosum DM8.1, SLF1797.7F-box domain
SLF15-2ptg0025165073603565798-3564539Solanum tuberosum DM8.1, SLF1597.7F-box domain
SLF16-2ptg0025165073605050596-5049416Solanum tuberosum DM8.1, SLF1699.3F-box domain

Nucleotide

Protein

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