Solanum andreanum PG3003 Assembly & Annotation

Overview

Analysis Name Solanum andreanum PG3003 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 1,271,197,709 bp
Contig number 2807
Contig N50 11,159,724 bp
Contig L50 25
Contig longest 49,203,400 bp
Assembly level Contig

Assembly

The Solanum andreanum PG3003 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) PG3003.fa.gz

Gene Predictions

The Solanum andreanum PG3003 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PG3003.gff.gz
CDS sequences (FASTA file) PG3003.cds.fa.gz
Protein sequences (FASTA file) PG3003.protein.fa.gz

Functional Analysis

Functional annotation for the Solanum andreanum PG3003 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_andreanum_PG3003.Pfam.tsv.gz

S genes

Summary

QueryContigSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF18atg010137823692888313-2889425Solanum tuberosum DM8.1, SLF1896.3F-box domain
SLF19Ψatg010137823692927718-2926604Solanum tuberosum DM8.1, SLF1994.9-
SLF13atg01232182889845038-843836Solanum tuberosum DM8.1, SLF1396.3F-box domain
SLF12Ψatg012321828891412566-1411399Solanum pennellii NM_001323464.1,
SLF12		93-
SLF6atg012321828891440283-1441425Solanum tuberosum DM8.1, SLF6-295.8F-box domain
SLF11atg03601100967438191-439360Solanum tuberosum DM8.1, SLF1195.4F-box domain
SLF9hptg000567056411100414-1101556Solanum tuberosum DM8.1, SLF997.7F-box domain
SLF21hptg000567056413308260-3309477Solanum tuberosum DM8.1, SLF2196.3F-box domain
SLF20hptg000567056413729754-3730920Solanum tuberosum DM8.1, SLF2096.7F-box domain
SLF7Ψhptg000567056413773624-3774786Solanum tuberosum DM8.1, SLF795-
SLF5hptg000567056413802072-3803238Solanum tuberosum DM8.1, SLF5-297.5F-box domain
S-RNasehptg000567056414405051-4404809,
4404695-4404270		Solanum tuberosum MZ561410.1,
SRNase-S7		93.4Ribonuclease T2 family
SLF12-2hptg000567056415289177-5288014Solanum tuberosum DM8.1, SLF1295.7F-box domain
SLF12-3hptg000567056415331627-5330467Solanum tuberosum DM8.1, SLF1295F-box domain
SLF5-2hptg000567056416554391-6555581Solanum tuberosum DM8.1, SLF595.6F-box domain
SLF17hptg0012225605567205-66024Solanum tuberosum DM8.1, SLF1798.1F-box domain
SLF23hptg0012225605577467-76310Solanum lycopersicoides KU960925.1,
SLF23		95.3F-box domain
SLF1hptg00122256055115790-116971Solanum tuberosum DM8.1, SLF191.6F-box domain
SLF6-2hptg0022309628910356-11501Solanum tuberosum DM8.1, SLF694.8F-box domain
SLF22hptg00223096289476957-475806Solanum tuberosum DM8.1, SLF22-295.8F-box domain
SLF5-3hptg002230962891391517-1390333Solanum tuberosum DM8.1, SLF597.9F-box domain
SLF12-4hptg002230962891431985-1433151Solanum tuberosum DM8.1, SLF1298F-box domain
SLF4Ψhptg002230962891538793-1537648Solanum peruvianum KJ814848.1,
SLF4		94.3-
SLF5-4hptg002230962891732067-1730898Solanum tuberosum DM8.1, SLF5-297.6F-box domain
SLF7-2hptg002230962891760324-1759161Solanum tuberosum DM8.1, SLF795.3F-box domain
SLF6-3Ψhptg002230962891769312-1768161Solanum tuberosum DM8.1, SLF692.2-
SLF20-2hptg002230962891785579-1784413Solanum tuberosum DM8.1, SLF2096.4F-box domain
SLF21-2hptg002230962892196021-2194801Solanum tuberosum DM8.1, SLF2196.3F-box domain
SLF19-2Ψptg00114772165529340112-29341225Solanum tuberosum DM8.1, SLF1995.2-
SLF18-2ptg00114772165529376308-29375196Solanum tuberosum DM8.1, SLF1896.3F-box domain
SLF13-2ptg00114772165542827977-42829179Solanum tuberosum DM8.1, SLF1396.5F-box domain
SLF12-5Ψptg00114772165543128947-43127789Solanum pennellii NM_001323464.1,
SLF12		94.1-
SLF6-4ptg00114772165543168884-43170008Solanum tuberosum DM8.1, SLF6-294.1F-box domain
SLF11-2ptg00114772165544792857-44791688Solanum tuberosum DM8.1, SLF1195.8F-box domain
SLF9-2Ψptg00114772165546466971-46468113Solanum tuberosum DM8.1, SLF997.7-
SLF15ptg0014312590071451952-1453211Solanum tuberosum DM8.1, SLF1597.6F-box domain
SLF16Ψptg0014312590072733721-2732541Solanum tuberosum DM8.1, SLF1697.8-
SLF17-2ptg00143125900730468491-30467310Solanum tuberosum DM8.1, SLF1797.8F-box domain
SLF1-2ptg00143125900731171293-31172474Solanum pennellii KJ814858.1,
SLF1		92.8F-box domain

Nucleotide

Protein

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