ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2021
De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme, by long-read sequencing.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- Transcriptional control of tomato fruit development and ripening.Journal of experimental botany · 2025Review
- Multiple fertility restorer loci for cytoplasmic male sterility caused by mitochondrial gene orf137 in tomato.Journal of experimental botany · 2025Article
- Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network.International journal of molecular sciences · 2025Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- Chromosome-level genome assembly of Solanum pimpinellifolium.Scientific data · 2024Article
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- Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits.Annual review of genetics · 2023Review
- Genome-Wide Evolutionary Characterization and Expression Analysis of Major Latex Protein (MLP) Family Genes in Tomato.International journal of molecular sciences · 2023Article
- Identification and Expression Analysis of the Alfin-like Gene Family in Tomato and the Role ofPlants (Basel, Switzerland) · 2023Article
- A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.AoB PLANTS · 2023Article
- Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal.Scientific data · 2023Article
- Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species.Nature genetics · 2023Article
- Vegetable biology and breeding in the genomics era.Science China. Life sciences · 2023Review
- Transcriptome analysis reveals the regulation of cyclic nucleotide-gated ion channels in response to exogenous abscisic acid and calcium treatment under drought stress in tomato.Frontiers in genetics · 2023Article
- A chromosome-scale and haplotype-resolved genome assembly of carnation (Frontiers in plant science · 2023Article
- Article
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Two independent allohexaploidizations and genomic fractionation in Solanales.Frontiers in plant science · 2022Article
- Genome-wide analysis of the WRKY gene family unveil evolutionary history and expression characteristics in tomato and its wild relatives.Frontiers in genetics · 2022Article
- The genome ofHorticulture research · 2022Article
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7 authors.
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Abstract
The ancestral tomato species are known to possess genes that are valuable for improving traits in breeding. Here, we aimed to construct high-quality de novo genome assemblies of Solanum pimpinellifolium 'LA1670' and S. lycopersicum var. cerasiforme 'LA1673', originating from Peru. The Pacific Biosciences (PacBio) long-read sequences with 110× and 104× coverages were assembled and polished to generate 244 and 202 contigs spanning 808.8 Mbp for 'LA1670' and 804.5 Mbp for 'LA1673', respectively. After chromosome-level scaffolding with reference guiding, 14 scaffold sequences corresponding to 12 tomato chromosomes and 2 unassigned sequences were constructed. High-quality genome assemblies were confirmed using the Benchmarking Universal Single-Copy Orthologs and long terminal repeat assembly index. The protein-coding sequences were then predicted, and their transcriptomes were confirmed. The de novo assembled genomes of S. pimpinellifolium and S. lycopersicum var. cerasiforme were predicted to have 71,945 and 75,230 protein-coding genes, including 29,629 and 29,185 non-redundant genes, respectively, as supported by the transcriptome analysis results. The chromosome-level genome assemblies coupled with transcriptome data sets of the two accessions would be valuable for gaining insights into tomato domestication and understanding genome-scale breeding.
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