Plastid genomic in neglected and unconventional botanical families as tool for genetic, evolutionary and phylogenetic analyses

• Ano de defesa: 2020
• Autor(a) principal: Pacheco, Túlio Gomes
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Universidade Federal de Viçosa
• Palavras-chave em Português: Passiflora cirrhiflora; Genômica; Evolução; Cloroplastos; Genética Vegetal
• Link de acesso: https://locus.ufv.br//handle/123456789/27917

Normally, the plastid genome (plastome) of land plants contains 100-130 genes, which are organized in a DNA molecule of 120-160 kb. The plastome sequencing molecule has been important for studies related to genetic, evolution, and phylogenetic analyses. Plastid genes are useful to unveil phylogenetic relationships between families and botanical orders, while fast- evolving regions (i.e., introns and intergenic spacers) are a great source of molecular markers to use in phylogenetic analyses of low taxa and genetic diversity analysis. Also, the analysis of complete plastomes allows us to uncover unusual features such as large inversions, gene losses, the active selection acting on plastid genes, and the prediction of RNA editing sites. However, plastomes of several angiosperms families have remained poorly studied. Thus, the objective of this study was the sequencing of the first complete plastomes of the families Tropaeolaceae (Tropaeolum pentaphyllum) and Bixaceae (Bixa orellana); and contribute to a better understanding of the plastome evolution in the genus Passiflora (Passifloraceae) via plastome sequecing of six species of the subgenus Passiflora and Passiflora cirrhiflora of the subgenus Deidamioides. This work reports a detailed characterization of the plastomes, including the analysis of several parameters: structure of the plastomes, gene content, genetic divergence, molecular markers, RNA editing sites, and phylogenetic aspects. B. orellana showed some specific features if compared with other Malvales, such as positive selection acting on psaI gene and 11 specific RNA editing sites. Similarly, T. pentapphyllum showed specific extensions of the matK and rpoA genes, and two specific RNA editing sites. The species of the subgenus Passiflora showed highly divergent genes (i.e. clpP and accD) and a significant polymorphism of gains and losses of RNA editing sites. In contrast, P. cirrhiflora and other species of the subgenus Deidamioides showed a conserved set of RNA editing sites. In general, the phylogenetic analyses performed here showed well-supported trees, but some inconsistencies remained to be elucidated by using a larger number of sampled taxons. A large amount of genomic data was provided by this study, which is useful in various analyzes related to genetics, evolution, biotechnology, and conservation of the species studied here and other related taxa. Keywords: Organelle DNA. Molecular markers. Plastome evolution.