Solanum peruvianum 'ZY61 (cultivar)' ASM2770506v1 Assembly & Annotation

Overview

Analysis Name Solanum peruvianum 'ZY61 (cultivar)' ASM2770506v1 Assembly & Annotation
Sequencing technology PacBio
Assembly method Canu v. 1.5
Release Date 2023-01-11
Reference Publication(s)

Li N, He Q, Wang J, Wang B, Zhao J, Huang S, Yang T, Tang Y, Yang S, Aisimutuola P, Xu R, Hu J, Jia C, Ma K, Li Z, Jiang F, Gao J, Lan H, Zhou Y, Zhang X, Huang S, Fei Z, Wang H, Li H, Yu Q. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat Genet. 2023 May;55(5):852-860. doi: 10.1038/s41588-023-01340-y.

Abstract

Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.

Assembly statistics

Genome size 867.5 Mb
Number of scaffolds 1,766
Scaffold N50 64.5 Mb
Scaffold L50 6
Number of contigs 3,654
Contig N50 676.7 kb
Contig L50 302
Assembly level Scaffold

Assembly

The Solanum peruvianum 'ZY61 (cultivar)' ASM2770506v1 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) S.peruvianum.genomic.fa.gz

Gene Predictions

The Solanum peruvianum 'ZY61 (cultivar)' ASM2770506v1 genome gene prediction files are available in FASTA format.

Downloads

Genes (GFF3 file) -
CDS sequences (FASTA file) S.peruvianum.cds.fa.gz
Protein sequences (FASTA file) S.peruvianum.pep.fa.gz

Functional Analysis

Functional annotation for the Solanum peruvianum 'ZY61 (cultivar)' ASM2770506v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_peruvianum_ZY61_ASM2770506v1.Pfam.tsv.gz

S genes

Summary

QueryChr/CtgSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF14ΨContig004283401932460-31293Solanum pennellii BK009220.1, SLF1498.5 -
SLF23Contig007862193111453-10296Solanum pimpinellifolium KU960927.1, SLF2399.1 F-box domain
SLF14-2ΨContig0141110021954632-55800Solanum pennellii BK009220.1, SLF1498.1 -
SLF4ΨContig01950511666-1207Solanum pimpinellifolium KJ814871.1, SLF494.0 -
S-RNaseContig021954654743731-43492,
43399-42974		Solanum lycopersicum
XM_004229015.1, RNase1		97.5 F-box domain
SLF12ΨContig024624399024806-23679Solanum lycopersicum SL2.31, SLF1297.9 -
SLF17ΨContig029417851113298-12133Solanum peruvianum KU960916.1, SLF1799.8 -
SLF16Sly01951381711070181-1071362Solanum lycopersicum SL2.31, SLF1698.4 F-box domain
SLF15Sly01951381713597123-3595864Solanum lycopersicum SL2.31, SLF1595.3 F-box domain
SLF12-2ΨSly019513817133114506-33115633Solanum lycopersicum SL2.31, SLF1297.9 -
S-RNase-2Sly019513817142459508-42459269,
42459176-42458751		Solanum lycopersicum
XM_004229015.1, RNase1		97.5 F-box domain
S-RNase-3Sly019513817142508818-42509057,
42509150-42509575		Solanum lycopersicum
XM_004229015.1, RNase1		97.5 F-box domain
SLF11Sly019513817143395707-43394541Solanum pennellii BK009223.1, SLF1198.8 F-box domain
SLF5Sly019513817143540466-43539297Solanum peruvianum KJ814849.1, SLF599.8 F-box domain
SLF6Sly019513817143549366-43548221Solanum lycopersicum KJ814944.1, SLF699.1 F-box domain
SLF22ΨSly019513817147213956-47215088Solanum pennellii BK009218.1, SLF2298.9 -
S-RNase-4Sly019513817149532434-49532664,
49532756-49533169		Solanum peruvianum
AB072464.1, S22-RNase		99.1 F-box domain
SLF2Sly019513817149922999-49921818Solanum habrochaites KJ814908.1, SLF2-S198.5 F-box domain
SLF6-2ΨSly019513817149982874-49981746Solanum peruvianum KJ814850.1, SLF697.7 -
SLF4-2Sly019513817151892677-51893843Solanum pimpinellifolium KJ814871.1, SLF494.9 F-box domain
SLF5-2Sly019513817151978379-51977189Solanum lycopersicoides KU987627.2, SLF590.4 F-box domain
SLF20Sly019513817152168034-52169200Solanum peruvianum KU960913.1, SLF2098.4 F-box domain
SLF7ΨSly019513817152410795-52411966Solanum peruvianum KJ814851.1, SLF796.1 -
SLF20-2ΨSly019513817152733338-52734500Solanum peruvianum KU960913.1, SLF2098.0 -
SLF21ΨSly019513817153413859-53412554Solanum peruvianum KU960914.1, SLF2199.0 -
SLF9Sly019513817154201007-54199865Solanum pimpinellifolium KJ814875.1, SLF998.9 F-box domain
SLF10ΨSly019513817154392002-54393228Solanum chilense KJ814888.1, SLF1098.1 -
SLF11-2Sly019513817157245409-57244237Solanum peruvianum KJ814854.1, SLF1199.1 F-box domain
SLF12-3Sly019513817157950950-57952113Solanum peruvianum KJ814855.1, SLF1299.1 F-box domain
SLF13Sly019513817159122409-59121207Solanum peruvianum KJ814856.1, SLF1399.9 F-box domain
SLF14-3ΨSly019513817162158350-62157169Solanum chilense KJ814892.1, SLF1499.9 -
SLF19Sly019513817172078110-72079219Solanum lycopersicum SL2.31, SLF1997.9 F-box domain
SLF18Sly019513817172097682-72096567Solanum lycopersicum SL2.31, SLF1898.7 F-box domain

Nucleotide

Protein

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