Nanopore sequencing of organellar genomes revealed heteroplasmy in simple thalloid and leafy liverworts

Abstract

Membrane-bound organelles, such as mitochondria and chloroplasts, have played a crucial role in the evolution of plant cells. In this study, we investigate the presence of heteroplasmy and genomic variation in liverworts, a group of non-vascular plants, using nanopore sequencing technology. We selected four liverwort species representing different lineages: <i>Riccia fluitans</i>, <i>Apopellia endiviifolia</i>, <i>Aneura pinguis</i>, and <i>Scapania undulata</i>. Through nanopore sequencing, we sequenced, assembled, and annotated the organellar genomes of selected liverwort species. The plastid genomes of <i>Riccia fluitans</i>, <i>Apopellia endiviifolia</i>, <i>Aneura pinguis</i>, and <i>Scapania undulata</i> exhibited high conservation with previously published genomes, while the mitogenome of <i>Scapania undulata</i> represents the first report for this species. The analysis of the liverwort organellar genomes revealed conserved gene content, structure, and order. We further investigated heteroplasmy within the liverwort species. The plastome analysis did not detect structural heteroplasmy, which is observed in some angiosperms but seems limited to seed plants. However, in the mitogenomes, we found evidence of heteroplasmy in <i>Aneura pinguis</i>, <i>Apopellia endiviifolia</i>, and <i>Scapania undulata</i>. The heteroplasmic sites in the mitogenomes were mainly represented by substitutions, indels, and short tandem repeat polymorphisms. Some of the identified substitutions resembled RNA editing patterns observed in liverworts. This study highlights the utility of nanopore sequencing for studying organellar genomes and detecting heteroplasmy in liverworts. The findings expand our understanding of organellar genomic variation in non-vascular plants and provide insights into the mechanisms underlying heteroplasmy in liverwort mitogenomes. Further research is needed to explore the functional significance of heteroplasmy and its implications for liverwort evolution and adaptation.