Expansions and contractions of the inverted repeat, as well as gene loss and potential pseudogenization shape plastome evolution in Hechtioideae (Bromeliaceae, Poales)

• Published in: Journal of systematics and evolution : JSE 2024-05, Vol.62 (3), p.421-437
• Main Authors: Ramírez‐Morillo, Ivón M., Espinosa‐Barrera, Laura A., Granados Mendoza, Carolina, Vera‐Paz, Sandra I., Díaz Contreras Díaz, Daniel D., Romero‐Soler, Katya J.
• Format: Article
• Language: English
• Subjects: Bromeliaceae; Cytosine; Evolution; Flowering; Flowering plants; Gene sequencing; Genomes; Hechtia; Hechtioideae; Inversions; Inverted repeat; ndh gene family; phylogenetic informativeness; Phylogenetics; phylogenomics; Phylogeny; plastid genome; Plastomes; structural rearrangements
• ISSN: 1674-4918; 1759-6831
• DOI: 10.1111/jse.13004

Full plastomes have recently proven to be a valuable data source for resolving recalcitrant phylogenetic relationships in the flowering plant family Bromeliaceae. The study of complete plastomes has additionally led to the discovery of new structural rearrangements and advanced our understanding of bromeliad plastome diversity and evolution. Here, we focus on the study of full plastomes of the bromeliad subfamily Hechtioideae to assess phylogenetic relationships, marker informativeness, and plastome structure and evolution. Using whole‐genome sequencing data, we de novo assembled and annotated new plastid genomes of 19 Hechtioideae species plus one representative each from the Pitcairnioideae and Puyoideae subfamilies and compared them with four additional available plastomes from other bromeliad subfamilies. Our phylogenetic analysis using complete plastome sequences not only recovered the three currently recognized genera of Hechtioideae as monophyletic, strongly supporting Mesoamerantha as sister of Bakerantha and Hechtia, but also improved statistical support at different phylogenetic depths within the subfamily. We identified a set of highly informative loci, some of them explored for the first time in Hechtioideae. Structural rearrangements, including expansions and contractions of the inverted repeats, large inversions, and gene loss and potential pseudogenization were detected mainly within the genus Hechtia. Evolutionary trait rate shifts were associated with the size and guanine–cytosine content of the small single copy and inverted repeats. Analysis of complete plastome sequences obtained by whole‐genome sequencing improved statistical support across different phylogenetic depths in Hechtioideae and allowed the identification of highly informative loci previously unexplored in this lineage. Our plastome comparative analysis allowed us to identify several structural rearrangements in the subfamily, including expansions and contractions of the inverted repeat, large inversions, gene loss, and potential pseudogenization. Evolutionary trait rate shifts were detected at different Hechtioideae lineages in the size and guanine–cytosine content of the small single copy and inverted repeats.