A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution
Abstract With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34...
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2019
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oai:doaj.org-article:ea43137793aa42d7be412aa51b4c8c9f2021-12-02T15:07:52ZA chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution10.1038/s41598-019-47985-w2045-2322https://doaj.org/article/ea43137793aa42d7be412aa51b4c8c9f2019-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-47985-whttps://doaj.org/toc/2045-2322Abstract With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.Lorenzo BarchiMarco PietrellaLuca VenturiniAndrea MinioLaura ToppinoAlberto AcquadroGiuseppe AndolfoGiuseppe ApreaCarla AvanzatoLaura BassolinoCinzia CominoAlessandra Dal MolinAlberto FerrariniLouise Chappell MaorEzio PortisSebastian Reyes-Chin-WoRiccardo RinaldiTea SalaDavide ScaglionePrashant SonawanePaola TononiEfrat Almekias-SieglElisa ZagoMaria Raffaella ErcolanoAsaph AharoniMassimo DelledonneGiovanni GiulianoSergio LanteriGiuseppe Leonardo RotinoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-13 (2019) |
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Medicine R Science Q Lorenzo Barchi Marco Pietrella Luca Venturini Andrea Minio Laura Toppino Alberto Acquadro Giuseppe Andolfo Giuseppe Aprea Carla Avanzato Laura Bassolino Cinzia Comino Alessandra Dal Molin Alberto Ferrarini Louise Chappell Maor Ezio Portis Sebastian Reyes-Chin-Wo Riccardo Rinaldi Tea Sala Davide Scaglione Prashant Sonawane Paola Tononi Efrat Almekias-Siegl Elisa Zago Maria Raffaella Ercolano Asaph Aharoni Massimo Delledonne Giovanni Giuliano Sergio Lanteri Giuseppe Leonardo Rotino A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution |
| description |
Abstract With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes. |
| format |
article |
| author |
Lorenzo Barchi Marco Pietrella Luca Venturini Andrea Minio Laura Toppino Alberto Acquadro Giuseppe Andolfo Giuseppe Aprea Carla Avanzato Laura Bassolino Cinzia Comino Alessandra Dal Molin Alberto Ferrarini Louise Chappell Maor Ezio Portis Sebastian Reyes-Chin-Wo Riccardo Rinaldi Tea Sala Davide Scaglione Prashant Sonawane Paola Tononi Efrat Almekias-Siegl Elisa Zago Maria Raffaella Ercolano Asaph Aharoni Massimo Delledonne Giovanni Giuliano Sergio Lanteri Giuseppe Leonardo Rotino |
| author_facet |
Lorenzo Barchi Marco Pietrella Luca Venturini Andrea Minio Laura Toppino Alberto Acquadro Giuseppe Andolfo Giuseppe Aprea Carla Avanzato Laura Bassolino Cinzia Comino Alessandra Dal Molin Alberto Ferrarini Louise Chappell Maor Ezio Portis Sebastian Reyes-Chin-Wo Riccardo Rinaldi Tea Sala Davide Scaglione Prashant Sonawane Paola Tononi Efrat Almekias-Siegl Elisa Zago Maria Raffaella Ercolano Asaph Aharoni Massimo Delledonne Giovanni Giuliano Sergio Lanteri Giuseppe Leonardo Rotino |
| author_sort |
Lorenzo Barchi |
| title |
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution |
| title_short |
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution |
| title_full |
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution |
| title_fullStr |
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution |
| title_full_unstemmed |
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution |
| title_sort |
chromosome-anchored eggplant genome sequence reveals key events in solanaceae evolution |
| publisher |
Nature Portfolio |
| publishDate |
2019 |
| url |
https://doaj.org/article/ea43137793aa42d7be412aa51b4c8c9f |
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