Solanum pennellii acc. LA0716

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum.

Local alignment search (blast)

Select sequence type, enter sequence and start search

• nucleotide sequence (BLAST-db: annotated genes including promoter/5'-region and 3'-region)
• protein sequence (BLAST-db: annotated proteins)

Publication

Read more about the Solanum pennellii acc. LA0716 genome:

Bolger et al. (2014)
The genome of the stress-tolerant wild tomato species Solanum pennellii
Nature Genetics 46, 1034-1038

Download data

Full set

• Protein sequences (FASTA format)
  Spenn_v2.0-protein.fasta.gz
  
• CDS sequences (FASTA format)
  Spenn_v2.0-cds.fasta.gz
  
• cDNA sequences (FASTA format)
  Spenn_v2.0-cdna.fasta.gz
  
• Gene models (GFF3-format)
  Spenn_v2.0-gene_models.gff3.gz
  
• Translation scaffold-referring names to (Spenn00g000000)-names
  Spenn_v2.0-gene_names.txt.gz

High confidence subset

• Protein sequences (FASTA format)
  Spenn_v2.0-HC_protein.fasta.gz
• CDS sequences (FASTA format)
  Spenn_v2.0-HC_cds.fasta.gz
• cDNA sequences (FASTA format)
  Spenn_v2.0-HC_cdna.fasta.gz
• Gene models (GFF3-format)
  Spenn_v2.0-HC_gene_models.gff.gz

More S.pennellii acc.LA0716 data and a genome browser are available at Sol Genomics Network.

Solanum lycopersicum cv. M82

The Solanum lycopersicum cv. M82 genome was published in conjunction with the Solanum pennellii genome. The S. lycopersicum cv. M82 genome was sequenced using the existing S. lycopersicum cv. Heinz genome as a reference. One paired-end library was created with an insert size of 190 bp and sequenced to provide 574 million reads totaling 47.4 billion bases. These data were initially aligned to the Heinz reference genome, and this alignment was further refined. The detected variants were then applied to the genome, and a further round of alignment was performed, where additional SNPs were detected and applied to create the final M82 genome.

Publication

Read more about the Solanum lycopersicum cv. M82 genome:

Bolger et al. (2014)
The genome of the stress-tolerant wild tomato species Solanum pennellii
Nature Genetics 46, 1034-1038

Download data

Full set

• Genomic DNA (FASTA format)
  Slyc_M82-genomic.fasta.gz

Sequencing raw data are available at the European Nucleotide Archive (ENA) under the project accession PRJEB6302.

Solanum lycopersicum cv. Moneyberg

A gap-free Solanum lycopersicum cv. Moneyberg genome provides insights into linkage drag during breeding. Modern tomato breeding has introduced genetic material from multiple related wild tomato species to provide genetically encoded resistance to abiotic and biotic stresses, including pandemic strains of Tobacco Mosaic virus (TMV). We applied PacBio HiFi and Oxford Nanopore (ONT) sequencing to independently develop highly contiguous assemblies of an inbred TMV-resistant cultivated tomato variety. The HiFi and ONT assemblies were merged to generate a long read only assembly with an N50 value of 68.5 Mbp where all twelve chromosomes were assembled as single contigs. The merged assembly is validated by chromosome conformation capture data and is highly consistent with previous tomato assemblies that made use of genetic maps or HiC for scaffolding. Our long read only assemblies reveal that a complex series of structural variants in the TMV resistance locus likely contributed to linkage drag of a 64.1 megabase pair region of wild DNA from Solanum peruvianum during tomato breeding.

Publication

Read more about the Solanum lycopersicum cv. Moneyberg genome:

van Rengs et al. (2022)
A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding
Plant J. 2022 Apr, 110(2): 572-588.

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Assemblies (FASTA format)

• Assembly from the HiFi-reads assembled with Canu v2.1.1 (HiCanu settings)
  Moneyberg_Canu.fasta.gz
• Assembly from the ONT-reads assembled with Flye v2.8.2 (default settings)
  Moneyberg_Flye.fasta.gz
• Assembly from the HiFi-reads assembled with Hifiasm 0.14.2 (default settings)
  Moneyberg_Hifiasm.fasta.gz
• Assembly from the ONT-reads assembled with NECAT 0.0.1_update20200803 (coverage 40x)
  Moneyberg_NECAT.fasta.gz
• Assembly by merging the contigs from Hifiasm and Canu with Quickmerge
  Moneyberg_Hifiasm+Canu.fasta.gz
• Assembly by merging the contigs from NECAT and Flye with Quickmerge
  Moneyberg_NECAT+Flye.fasta.gz
• Assembly from the Hifiasm + Canu assembly and NECAT + Flye assembly
  MbTMV.fasta.gz

Solanum pennellii acc. LA5240

Solanum pennellii acc. LA5240 is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. In contrast to Solanum pennellii acc. LA0716, the accession LA5240 does not appear to exhibit any dwarfed, necrotic leaf phenotype when introgressed into modern tomato cultivars.

Recent updates in Oxford Nanopore technology (ONT, R9.4) have made it possible to obtain gigabases of sequence data from a single flow cell. However, unlike other next generation sequencing technology, ONT-based sequencing does not require any a priori capital investments. We therefore evaluated whether ONT can be used to analyze plant genomes. To this aim, we sequenced and assembled the spuriously identified accession LA5240 (LYC1722) of Solanum pennellii.

Download data

• Protein sequences (FASTA format)
  Spenn_LA5240-protein.fasta
• cDNA sequences (FASTA format)
  Spenn_LA5240-gene_models.transcript
• Gene models (GFF3-format)
  Spenn_LA5240-gene_models.gff

Local alignment search (blast)

Select sequence type, enter sequence and start search

• nucleotide sequence (BLAST-db: scaffolds)
• protein sequence (BLAST-db: annotated proteins)

Publication

Read more about the Solanum pennellii acc. LA5240 genome:

Schmidt et al. (2017)
De novo assembly of a new Solanum pennellii accession using Nanopore sequencing
Plant Cell 29(10), 2336-2348