ArticlePlant communications2023
Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants.
Article in Plant communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 65 citations in OpenAlex.
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- Functional diversification of WRINKLED3 integrates fatty acid metabolism with insecticidal acylsugar production in Solanaceae species.Nature communications · 2026Article
- Large-scale plant genomic identification and analysis uncoverHorticulture research · 2026Article
- A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation.bioRxiv : the preprint server for biology · 2026Article
- Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses inPlants (Basel, Switzerland) · 2025Article
- MYB regulator of "colorless" flavonols underlies the evolution of red flowers in Iochroma (Solanaceae).G3 (Bethesda, Md.) · 2025Article
- Chloroplast Genome Characterization ofEcology and evolution · 2025Article
- Evolutionarily New Solanaceous DCL2 Family Members Acquire Functions in Tomato.Molecular plant pathology · 2025Article
- Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen.The Plant cell · 2025Article
- S-RNase-based self-incompatibility in angiosperms: Degradation, condensation, and evolution.Plant physiology · 2025Review
- Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis.Nature communications · 2025Article
- Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum.G3 (Bethesda, Md.) · 2025Article
- Genomic Phylogenetic Analysis ofEcology and evolution · 2025Article
- Enzymatic twists evolved stereo-divergent alkaloids in the Solanaceae family.Nature communications · 2025Article
- Genome assembly of Stewartia sinensis reveals origin and evolution of orphan genes in Theaceae.Communications biology · 2025Article
- Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Incorporation of nitrogen in antinutritional Solanum alkaloid biosynthesis.Nature chemical biology · 2025Article
- Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae).BMC genomics · 2024Article
- Evolutionary History and Ecology ofEcology and evolution · 2024Article
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Authors and funding
11 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.
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