ArticlePlant communications2025
Solanaceae pan-genomes reveal extensive fractionation and functional innovation of duplicated genes.
Article in Plant communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Genome-Wide Identification of CRK Family Members in Solanaceae Crops and Functional Characterization ofCurrent issues in molecular biology · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Article
- Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Toward telomere-to-telomere genomics in Fabaceae: Unlocking comparative and functional insights into symbiotic nitrogen fixation.Cell genomics · 2026Review
- Rewiring Steroidal Metabolic Pathways for Diosgenin Production in Solanum nigrum.Plant biotechnology journal · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Identification and comprehensive characterization of the OVATE family protein in litchi.BMC plant biology · 2026Article
- Molecular mechanisms and breeding strategies for heat tolerance in vegetable crops under global warming.Horticulture research · 2026Article
- Comparative analysis of seven types of phosphate transporters in forty species from the phylogenetic and transcriptomic perspective.PloS one · 2026Article
- EucaMOD: a comprehensive multi-omics database for functional genomics research and molecular breeding of fast-growing eucalyptus trees.The Plant journal : for cell and molecular biology · 2025Article
- Genome-wide analysis of the CML gene family and its response to cold stress in Curcuma alismatifolia.BMC plant biology · 2025Article
- Comparative Transcriptome Reveals Conserved Gene Expression in Reproductive Organs in Solanaceae.International journal of molecular sciences · 2025Article
- Mitigating Response ofPlants (Basel, Switzerland) · 2025Article
- From map to blueprint: the plant pan-genome unraveling genetic mysteries and powering precision breeding.Frontiers in plant science · 2025Review
Corrections and comments
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Authors and funding
9 authors.
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Abstract
The Solanaceae family contains many agriculturally important crops, including tomato, potato, pepper, and tobacco, as well as other species with potential for agricultural development, such as the orphan crops groundcherry, wolfberry, and pepino. Research progress varies greatly among these species, with model crops like tomato being far ahead. This disparity limits the broader agricultural application of other Solanaceae species. In this study, we constructed an interspecies pan-genome for the Solanaceae family and identified various gene retention patterns. Our findings reveal that the activity of specific transposable elements is closely associated with gene fractionation and transposition. The pan-genome was further resolved at the level of T subgenomes, which were generated by Solanaceae-specific paleo-hexaploidization (T event). We demonstrate substantial gene fractionation (loss) and divergence events following ancient duplications. For example, all class A and E flower model genes in Solanaceae originated from two tandemly duplicated genes, which expanded through the γ and T events before fractionating into 10 genes in tomato, each acquiring distinct functions critical for fruit development. Based on these results, we developed the Solanaceae Pan-Genome Database (SolPGD, http://www.bioinformaticslab.cn/SolPGD), which integrates datasets from both inter- and intra-species pan-genomes of Solanaceae. These findings and resources will facilitate future studies of solanaceous species, including orphan crops.
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