Evolution of 101 Apocynaceae plastomes and phylogenetic implications

Area of Science:

• Botany
• Plant Systematics
• Molecular Evolution

Background:

• Apocynaceae is a species-rich angiosperm family with an incompletely resolved backbone phylogeny.
• The evolution of plastome structure across the entire Apocynaceae family remains understudied.

Purpose of the Study:

• To reconstruct the backbone phylogeny of Apocynaceae using a comprehensive plastome dataset.
• To investigate the evolutionary patterns of plastome structure within the family.

Main Methods:

• Comparative analysis of 101 complete plastomes representing 26 of 27 Apocynaceae tribes.
• Phylogenetic analyses using a combined plastid data matrix of 77 protein-coding genes from 162 taxa.
• Identification of variable genes and non-coding regions, and analysis of inverted repeat (IR) boundary variations.

Main Results:

• A well-resolved backbone phylogeny for Apocynaceae comprising 15 clades was established.
• Multiple expansion events of IRs over SC regions were identified in Alyxieae, Ceropegieae, and Marsdenieae.
• Variable coding genes (e.g., accD, matK) and non-coding regions were identified, with some tribes and genera found to be non-monophyletic.

Conclusions:

• The study provides a robust phylogenetic framework for Apocynaceae, clarifying relationships between major clades.
• Insights into the dynamic evolution of plastome structure, particularly IR expansion, were gained.
• The findings highlight areas of taxonomic uncertainty within the family, such as non-monophyletic tribes and genera.