Solanum vernei PG4036 Assembly & Annotation

Overview

Analysis Name Solanum vernei PG4036 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 1,411,055,966 bp
Contig number 2998
Contig N50 7,932,388 bp
Contig L50 36
Contig longest 55,734,203 bp
Assembly level Contig

Assembly

The Solanum vernei PG4036 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) PG4036.fa.gz

Gene Predictions

The Solanum vernei PG4036 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PG4036.gff.gz
CDS sequences (FASTA file) PG4036.cds.fa.gz
Protein sequences (FASTA file) PG4036.protein.fa.gz

Functional Analysis

Functional annotation for the Solanum vernei PG4036 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_vernei_PG4036.Pfam.tsv.gz

S genes

Summary

QueryContigSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF15atg020718138631311585-1310326Solanum tuberosum DM8.1, SLF1597.8 F-box domain
SLF16Ψatg021713636451166740-1165560Solanum tuberosum DM8.1, SLF1698.1 -
SLF19Ψatg0243660683598738-599851Solanum tuberosum DM8.1, SLF1994.8 -
SLF18atg0243660683650484-649369Solanum tuberosum DM8.1, SLF1896.7 F-box domain
SLF9hptg0026188732381868760-1869902Solanum tuberosum DM8.1, SLF998.1 F-box domain
SLF21hptg0026188732383715799-3717019Solanum tuberosum DM8.1, SLF2199.0 F-box domain
SLF20hptg0026188732384166940-4168106Solanum tuberosum DM8.1, SLF2099.4 F-box domain
SLF6Ψhptg0026188732384214118-4215259Solanum tuberosum DM8.1, SLF692.6 -
SLF7hptg0026188732384232987-4234156Solanum tuberosum DM8.1, SLF797.9 F-box domain
SLF5hptg0026188732384335436-4336605Solanum tuberosum DM8.1, SLF5-298.4 F-box domain
SLF5-2hptg0026188732384631012-4632190Solanum tuberosum DM8.1, SLF592.0 F-box domain
SLF12hptg0026188732384840711-4839545Solanum tuberosum DM8.1, SLF1297.5 F-box domain
S-RNasehptg0026188732387040544-7040771,
7040885-7041313		Solanum tuberosum
MZ561417.1, SRNase-S14		98.2 Ribonuclease T2 family
SLF6-2hptg0026188732387404283-7403138Solanum lycopersicoides
KU987626.1, SLF6		95.7 F-box domain
SLF17hptg0026188732388139353-8138172Solanum tuberosum DM8.1, SLF1797.7 F-box domain
SLF23hptg0026188732388200377-8199220Solanum lycopersicoides
KU960925.1, SLF23		94.7 F-box domain
SLF22hptg0026188732389042028-9043167Solanum tuberosum DM8.1, SLF2298.8 F-box domain
SLF22-2hptg00261887323811906785-11905646Solanum tuberosum DM8.1, SLF2298.6 F-box domain
SLF22-3hptg00261887323814475296-14474145Solanum tuberosum DM8.1, SLF22-296.0 F-box domain
SLF17-2hptg00261887323815143257-15144423Solanum tuberosum DM8.1, SLF1797.3 F-box domain
S-RNase-2hptg00261887323815791129-15790893,
15790805-15790392		Solanum chacoense
S69589.1, ScS11-RNase		98.8 Ribonuclease T2 family
SLF5-3hptg00261887323816857690-16856506Solanum tuberosum DM8.1, SLF597.6 F-box domain
SLF12-2hptg00261887323816911643-16912809Solanum tuberosum DM8.1, SLF1298.7 F-box domain
SLF5-4hptg00261887323817232744-17231575Solanum tuberosum DM8.1, SLF5-298.8 F-box domain
SLF7-2hptg00261887323817312197-17311028Solanum tuberosum DM8.1, SLF797.6 F-box domain
SLF6-3Ψhptg00261887323817334893-17333751Solanum tuberosum DM8.1, SLF692.1 -
SLF20-2hptg00261887323817396330-17395164Solanum tuberosum DM8.1, SLF2099.2 F-box domain
SLF13hptg00261887323818035269-18036471Solanum tuberosum DM8.1, SLF1399.4 F-box domain
SLF6-4Ψhptg00261887323818404114-18405264Solanum tuberosum DM8.1, SLF6-295.3 -
SLF6-5Ψhptg00453301181493306-492144Solanum tuberosum DM8.1, SLF6-296.1 -
SLF13-2hptg00453301181829197-827989Solanum tuberosum DM8.1, SLF1398.7 F-box domain
SLF16-2Ψptg0011145231932024984-2023804Solanum tuberosum DM8.1, SLF1698.0 -
SLF15-2ptg001356788314890249-4888990Solanum tuberosum DM8.1, SLF1597.8 F-box domain
SLF18-2ptg00264608132230246067-30244952Solanum tuberosum DM8.1, SLF1897.1 F-box domain
SLF21-2ptg00264608132242666311-42665091Solanum tuberosum DM8.1, SLF2199.0 F-box domain
SLF9-2ptg00264608132244365938-44364796Solanum tuberosum DM8.1, SLF998.2 F-box domain

Nucleotide

Protein

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