Mitochondrial phylogenomics of liverworts

Premise: Liverworts, with approximately 7,300 species worldwide, exhibit
remarkable morphological diversity, in terms of growth form, ontogeny and
architecture. Based on phylogenetic inferences drawn from DNA data,
including recent genomic-scale data, the relationships among families and
orders have been constantly revised and refined, although new topological
incongruences have emerged. The liverwort mitochondrial genome exhibits
lower average substitution rates compared to their nuclear and plastid
genomes, and shows less structural variation, suggesting its suitability
for inferring relationships at higher taxonomic levels. Methods: The
mitochondrial genomes of 112 liverworts were sequenced, covering 105
species, 52 families and 18 orders. We analysed the structures of the
liverwort mitogenomes using Mauve alignment. Maximum likelihood and
Bayesian inference methods were used to infer a family-level phylogeny of
liverworts. Results: We assembled the complete mitochondrial genome for 23
species and identified four new structural variants. Phylogenetic
inferences from mitochondrial genome sequences confirmed the monophyly of
most suprafamilial taxa, with the expectations of Porellales, Ptilidiales,
and Pelliidae. Herzogianthus (Ptilidiales) was well-supported as a sister
group to Jungermanniales sensu lato, rather than forming a monophyletic
lineage with Ptilidium (Ptilidiales). Given its distinct morphological
traits, this genus should be singled out and elevated to a new order.
Conclusions: The overall architecture of liverwort mitogenomes remains
highly conserved, with taxa that diverged over 470 Mya still having
co-linear mitogenomes. This study provides a genetic resource for future
evolutionary research across the liverworts and highlights the utility of
mitogenome across lineages diversifying for 470 Mya, including for
family‐level classification.