Multipartite mitochondrial genome evolution in Halophila seagrasses: repeat-driven structural plasticity and...

The degradation of seagrass beds, which serve as pivotal indicators of coastal ecosystem health, has emerged as a critical reflection of global nearshore environmental stress. In this study, we employed two closely related seagrass species, Halophila beccarii and H. ovalis, as case studies to investigate the structural and evolutionary dynamics of their mitochondrial genomes through comparative genomics and evolutionary analyses.

Our findings reveal striking structural disparities in the mitochondrial genomes of the two species: H. beccarii comprises 28 free circular elements totaling 1.98 Mb, whereas H. ovalis harbors 12 circular units spanning 0.58 Mb. Codon usage analysis demonstrated a significant A/U preference at the third position of high-frequency codons. Analyses of relative substitution rates (Ka/Ks) showed that the nad3 gene consistently exhibited ratios greater than 1 in both marine-freshwater pairwise comparisons and across the phylogeny, distinguishing it from other mitochondrial genes. Halophila species showed a reduced complement of RNA editing sites. Specifically, genes nad3 and nad6 in H. beccarii, and cox1, nad3, and nad6 in H. ovalis completely lacked RNA editing under the experimental conditions employed.

Collectively, this work characterizes the diverse mitogenomic architecture in seagrasses, offering a genomic foundation for future studies on seagrass evolution and environmental response.