Mitochondrial phylogenomics of liverworts
Data files
May 10, 2024 version files 5.08 MB
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1_MrBayes_trimmed.zip
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1_MrBayes.nex.con.zip
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1_RAxML_bipartitions.zip
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1_RAxML_trimmed.zip
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3_MrBayes_trimmed.zip
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3_MrBayes.nex.con.zip
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3_RAxML_bipartitions.zip
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3_RAxML_trimmed.zip
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captured_genes.zip
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complete_assemblies.zip
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README.md
Abstract
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.