Abstract
BackgroundIn contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available mt genomes of 18 liverwort accessions representing nine genera and five orders are syntenous except for Gymnomitrion concinnatum whose genome is characterized by two rearrangements. Here, we expanded the number of assembled liverwort mt genomes to 47, broadening the sampling to 31 genera and 10 orders spanning much of the phylogenetic breadth of liverworts to further test whether the evolution of the liverwort mitogenome is overall static.ResultsLiverwort mt genomes range in size from 147 Kb in Jungermanniales (clade B) to 185 Kb in Marchantiopsida, mainly due to the size variation of intergenic spacers and number of introns. All newly assembled liverwort mt genomes hold a conserved set of genes, but vary considerably in their intron content. The loss of introns in liverwort mt genomes might be explained by localized retroprocessing events. Liverwort mt genomes are strictly syntenous in genome structure with no structural variant detected in our newly assembled mt genomes. However, by screening the paired-end reads, we do find rare cases of recombination, which means multiple concurrent genome structures may exist in the vegetative tissues of liverworts. Our phylogenetic analyses of the nuclear encoded double stand break repair protein families revealed liverwort-specific subfamilies expansions.ConclusionsThe low repeat recombination level, selection, along with the intensified nuclear surveillance, might together shape the structural evolution of liverwort mt genomes.
Highlights
In contrast to the highly labile mitochondrial genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant
Liverwort mitogenomes are small in size but abundant in genes Assemblies of high throughput sequences from total DNA extracts yielded complete circular mt genomes for 29 liverworts, representing 27 genera, 23 families, and 10 orders, of which five orders were newly sampled for their mt genomes
Including the published mt genomes from 13 species, complete liverwort mt genomes are available from 37 species, 31 genera, and 10 orders (Additional file 2: Table S2)
Summary
In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. Vascular plant mt genomes contain a variable set of introns, ranging in numbers from three (Viscum album [3]) to 37 (Selaginella moellendorffii [15]), with an average of 21. Each bryophyte group appears to hold a stable set of introns that parallels their conserved evolution of mt genomes of overall structure, recent small-scale mitogenomic studies provided evidences for distinct intron losses in leafy liverworts, and suggested retroprocessing as the likely causes [13]. Comprehensive studies with expanded taxon samplings are still needed to provide the framework for reconstructing the evolution of introns in liverwort mt genomes, and to assess the underlying causes for their variation in number
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