Using a combination of Illumina sequencing and optical mapping, we produced a high quality genome draft of the eggplant ( S. melongena L.) ’67/3’ inbred line. The sequence was anchored to the 12 chromosomes using a Recombinant Inbred (RIL) population and used for comparative studies with the tomato, potato and pepper genomes. The eggplant genome is 1.2 Gbases long and contains 39,922 predicted genes, of which 4,607 are of organellar origin and 3,234 are paralogs generated by the whole genome ‘T’ triplication event. The latter are enriched in transcription factor genes in all four Solanaceae studied, suggesting that the ‘T’ event has increased the diversity of regulatory genes, contributing to the vast morphological and physiological diversity of Solanaceae. A second mechanism contributing to functional diversity is the rapid evolution of miRNA:mRNA regulatory pairs, whose vast majority was predicted computationally to be species-specific, rather than conserved across the Solanaceae family. A reconstruction of the ancestral Solanaceae, Solanum and Potatoe genome complements highlighted the chromosome rearrangements that led to the present-day chromosomal composition of the four Solanaceae. The four genomes underwent explosive colonization by transposable elements at very different times, with pepper and eggplant being the most ancient and recent (~3 mya and (0.3 mya). Orthologs of tomato ripening-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 and chlorophyll degradation had more evolutionary conserved patterns of expression than those involved in ethylene biosynthesis, light perception, carotenoid/phenylpropanoid biosynthesis, and fruit softening. Species-specific tandem amplification of R genes provided a structural basis for the differential pathogen sensitivity of Solanaceae, while the absence of a glycoalkaloid gene cluster on chromosome 12 is the likely cause for the absence of this class of secondary metabolites in pepper.
The eggplant genome reveals key events in Solanaceae evolution
BARCHI, Lorenzo;ACQUADRO, Alberto;COMINO, CINZIA;PORTIS, Ezio;RINALDI, RICCARDO;SCAGLIONE, DAVIDE;LANTERI, Sergio;
2016-01-01
Abstract
Using a combination of Illumina sequencing and optical mapping, we produced a high quality genome draft of the eggplant ( S. melongena L.) ’67/3’ inbred line. The sequence was anchored to the 12 chromosomes using a Recombinant Inbred (RIL) population and used for comparative studies with the tomato, potato and pepper genomes. The eggplant genome is 1.2 Gbases long and contains 39,922 predicted genes, of which 4,607 are of organellar origin and 3,234 are paralogs generated by the whole genome ‘T’ triplication event. The latter are enriched in transcription factor genes in all four Solanaceae studied, suggesting that the ‘T’ event has increased the diversity of regulatory genes, contributing to the vast morphological and physiological diversity of Solanaceae. A second mechanism contributing to functional diversity is the rapid evolution of miRNA:mRNA regulatory pairs, whose vast majority was predicted computationally to be species-specific, rather than conserved across the Solanaceae family. A reconstruction of the ancestral Solanaceae, Solanum and Potatoe genome complements highlighted the chromosome rearrangements that led to the present-day chromosomal composition of the four Solanaceae. The four genomes underwent explosive colonization by transposable elements at very different times, with pepper and eggplant being the most ancient and recent (~3 mya and (0.3 mya). Orthologs of tomato ripening-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 and chlorophyll degradation had more evolutionary conserved patterns of expression than those involved in ethylene biosynthesis, light perception, carotenoid/phenylpropanoid biosynthesis, and fruit softening. Species-specific tandem amplification of R genes provided a structural basis for the differential pathogen sensitivity of Solanaceae, while the absence of a glycoalkaloid gene cluster on chromosome 12 is the likely cause for the absence of this class of secondary metabolites in pepper.
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