The Eggplant Genome Reveals Key Events in Solanaceae Evolution

From The Eggplant Genome Consortium.

A high quality genome draft of eggplant (S. melongena L.) was produced and anchored to the 12 chromosomes. The eggplant genome contains 34,916 predicted genes, of which 3,234 are paralogs generated by the ‘T’ whole genome triplication event. These paralogs are enriched in transcription factor-encoding genes in tomato, potato, pepper and eggplant, suggesting that the ‘T’ event contributed to Solanaceae functional diversification. A second diversifying mechanism is the rapid evolution of miRNA:mRNA regulatory pairs, whose vast majority are species-specific, rather than conserved across the Solanaceae family. A reconstruction of the ancestral Solanaceae, Solanum and Potatoe genomes highlighted the rearrangements that led to the chromosome complements of extant Solanaceae. The four genomes underwent recent (~3 mya in pepper and ~0.3 mya in eggplant) colonization by transposable elements after the separation of the main clades. Fruit-associated genes showed different patterns of regulation across the Solanaceae family: genes involved in ethylene-independent ripening control, ethylene sensing and signal transduction, light signal transduction, chlorophyll degradation and cuticle biosynthesis had more evolutionary conserved patterns of expression than those involved in ethylene biosynthesis, light perception, carotenoid/phenylpropanoid biosynthesis, and fruit softening. Overexpression of TAGL1 in tomato and eggplant results in similar developmental phenotypes (sepal expansion), but in different biochemical ones (lycopene vs flavonol accumulation). Species-specific tandem amplification of R genes provided a basis for the differential pathogen sensitivity of Solanaceae, while the absence of a glycoalkaloid gene cluster on chromosome 12 provided a basis for the absence of these secondary metabolites in pepper.