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Comparative Organellar Genomics of Pellidae: Insights into Codon Usage, Nucleotide Diversity, and Structural Evolution

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dc.abstract.enLiverwort organellar genomes are generally highly conserved, but the subclass Pellidae (simple thalloids) shows unusual variation. This ancient yet unexplored lineage of simple thalloid liverworts provides an excellent model for investigating organellar genome evolution. In this study, we assembled four new plastid and four new mitochondrial Pellidae genomes using Oxford Nanopore sequencing, supplementing 86 plastomes and 82 mitogenomes from databases. We assessed nucleotide diversity and codon usage, and inferred phylogenies using IQ-TREE with fossil-calibrated dating. Plastomes ranged 120.6–126.5 kb, and mitogenomes 109–180 kb, with Apopellia endiviifolia featuring an exceptionally reduced mitogenome (~109 kb). Native RNA sequencing enabled a revised annotation of the mitochondrial atp1 gene in Apopellia, revealing two introns (previously thought absent) and reducing the intergenic region share to 36.26%, the lowest known among liverworts. Comparative analyses revealed contrasting evolutionary dynamics between organelles: Plastomes displayed higher nucleotide diversity and phylogenetically inconsistent codon usage patterns, likely influenced by compositional bias, whereas mitogenomes were more conserved and largely consistent with established phylogenetic relationships among the orders. Phylogenomic analyses yielded discordant topologies: Chloroplast data recovered Pellidae as a monophyletic clade, whereas mitochondrial data placed Pelliales (Pellia/Apopellia) as basal Jungermanniopsida, rendering Pellidae paraphyletic. Within Pellidae-relevant clades, several major divergences were dated to the Carboniferous–Permian, but with systematic chloroplast–mitochondrial offsets. These results highlight recurrent organellar incongruence and the dynamic evolutionary history of Pellidae organellar genomes.
dc.affiliationWydział Rolnictwa, Ogrodnictwa i Biotechnologii
dc.affiliation.instituteKatedra Botaniki
dc.contributor.authorCzochór, Wiktoria
dc.contributor.authorKoczwara, Kamil
dc.contributor.authorPupek, Natan
dc.contributor.authorGórski, Piotr
dc.contributor.authorSzablińska, Joanna
dc.contributor.authorSawicki, Jakub
dc.contributor.authorSzczecińska, Monika
dc.date.access2026-04-13
dc.date.accessioned2026-04-13T09:50:38Z
dc.date.available2026-04-13T09:50:38Z
dc.date.copyright2026-03-24
dc.date.issued2026
dc.description.abstract<jats:p>Liverwort organellar genomes are generally highly conserved, but the subclass Pellidae (simple thalloids) shows unusual variation. This ancient yet unexplored lineage of simple thalloid liverworts provides an excellent model for investigating organellar genome evolution. In this study, we assembled four new plastid and four new mitochondrial Pellidae genomes using Oxford Nanopore sequencing, supplementing 86 plastomes and 82 mitogenomes from databases. We assessed nucleotide diversity and codon usage, and inferred phylogenies using IQ-TREE with fossil-calibrated dating. Plastomes ranged 120.6–126.5 kb, and mitogenomes 109–180 kb, with Apopellia endiviifolia featuring an exceptionally reduced mitogenome (~109 kb). Native RNA sequencing enabled a revised annotation of the mitochondrial atp1 gene in Apopellia, revealing two introns (previously thought absent) and reducing the intergenic region share to 36.26%, the lowest known among liverworts. Comparative analyses revealed contrasting evolutionary dynamics between organelles: Plastomes displayed higher nucleotide diversity and phylogenetically inconsistent codon usage patterns, likely influenced by compositional bias, whereas mitogenomes were more conserved and largely consistent with established phylogenetic relationships among the orders. Phylogenomic analyses yielded discordant topologies: Chloroplast data recovered Pellidae as a monophyletic clade, whereas mitochondrial data placed Pelliales (Pellia/Apopellia) as basal Jungermanniopsida, rendering Pellidae paraphyletic. Within Pellidae-relevant clades, several major divergences were dated to the Carboniferous–Permian, but with systematic chloroplast–mitochondrial offsets. These results highlight recurrent organellar incongruence and the dynamic evolutionary history of Pellidae organellar genomes.</jats:p>
dc.description.accesstimeat_publication
dc.description.bibliographyil., bibliogr.
dc.description.financepublication_nocost
dc.description.financecost0,00
dc.description.if4,1
dc.description.number7
dc.description.points70
dc.description.versionfinal_published
dc.description.volume15
dc.identifier.doi10.3390/plants15070997
dc.identifier.issn2223-7747
dc.identifier.urihttps://sciencerep.up.poznan.pl/handle/item/8073
dc.identifier.weblinkhttps://www.mdpi.com/2223-7747/15/7/997
dc.languageen
dc.pbn.affiliationagriculture and horticulture
dc.relation.ispartofPlants
dc.relation.pagesart. 997
dc.rightsCC-BY
dc.sciencecloudnosend
dc.share.typeOPEN_JOURNAL
dc.subject.enPellidae
dc.subject.enliverworts
dc.subject.enatp1 gene
dc.subject.enorganellar genomes
dc.subject.enphylogenomics
dc.titleComparative Organellar Genomics of Pellidae: Insights into Codon Usage, Nucleotide Diversity, and Structural Evolution
dc.title.volumeSpecial Issue Diversity and Classification of Bryophytes
dc.typeJournalArticle
dspace.entity.typePublication
oaire.citation.issue7
oaire.citation.volume15