A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae

Autor(es)

Romeiro-Brito, Monique ; Telhe, Milena Cardoso ; Amaral, Danilo Trabuco ; Franco, Fernando Faria ; Moraes, Evandro Marsola

• Tipo de documento: Artigo Científico
• Fonte: GENES; v. 13, n. 4, p. 15-pg., 2022-04-01.

Resumo

The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family. (AU)

• Processo FAPESP: 19/11233-2 - Filogenia, biogeografia e evolução de caracteres dos gêneros Melocactus link & Otto e Discocactus Pfeiff (Cactaceae)
• Beneficiário: Milena Cardoso Telhe
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto
• Processo FAPESP: 18/03428-5 - Dimensions US-BIOTA-Sao Paulo: características preditoras da diversificação adaptativa na Diagonal Seca Brasileira
• Beneficiário: Vera Nisaka Solferini
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOTA - Temático
• Processo FAPESP: 19/03211-9 - Filogenia, biogeografia e diversificação de cactos na América do Sul
• Beneficiário: Evandro Marsola de Moraes
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOTA - Regular
• Processo FAPESP: 18/06937-8 - Filogenia, biogeografia e diversificação de cactos da América do Sul com enfoque na Tribo Cereeae (Cactaceae)
• Beneficiário: Monique Romeiro Brito
• Modalidade de apoio: Bolsas no Brasil - Doutorado