Complete mitochondrial genomes of the two high-valued bromeliads: comparative genomics and evolutionary insights

The Bromeliaceae family contains many horticulturally and economically important species, including Aechmea fasciata and pineapple (Ananas comosus). Compared to their well-studied chloroplast and nuclear genomes, the mitogenomes of bromeliads remain largely unexplored, hindering a full understanding of their organellar evolution and phylogenetic relationships. This study provides the first complete mitogenome assemblies and a comparative analysis for these two high-value bromeliads, revealing their phylogenetic affinities. Our findings suggested that the mitogenomes of Ae. fasciata and An. comosus both exhibit a simple master circle structure. They were 0.93–1.16 Mb in length, containing similar protein-coding genes (PCGs) (42–44), 39 tRNA genes, and three rRNA genes. Notably, the synonymous codons usage analysis revealed a preference for A/U endings, and a total of 542–548 RNA editing sites were detected. Most PCGs were under purifying selection, indicating a strong evolutionary constraint to preserve functional integrity. Additionally, the ATP synthase gene exhibited high nucleotide diversity, suggesting that such genes may need further investigation in the context of future CMS-related studies. Phylogenetically, analyses based on shared PCGs provided robust support for the clustering relationships within Bromeliaceae, confirming that An. comosus and Ae. fasciata form a distinct clade and are separate from Puya raimondii. This study establishes a crucial comparative genomic framework for Bromeliaceae, providing valuable genetic resources for future evolutionary studies and potential marker-assisted breeding applications.