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Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates.
TLDR
The breadth of IR boundary shifts in land plants is explored and it is demonstrated that synonymous substitution rates are, on average, 3.7 times slower in IR genes than in SC genes, which provides strong evidence that the duplicative nature of the IR reduces the substitution rate within this region.
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Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among…
TLDR
Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns, demonstrating the power of using rare genomic structuralChanges in cases where molecular data fail to provide strong phylogenetic resolution.
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Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution.
TLDR
By conducting the first measurements of rates of DNA turnover in seed plant mitogenomes, it is discovered that turnover rates vary by orders of magnitude among species.
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Unprecedented heterogeneity in the synonymous substitution rate within a plant genome.
TLDR
This work sequenced the complete mitochondrial and plastid genomes from the bugleweed, Ajuga reptans, and uncovered a 340-fold range of synonymous substitution rate variation among Ajuga mitochondrial genes, by far the largest amount of synonymous rate heterogeneity ever reported for a genome.
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Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution
TLDR
Competitive genomic studies demonstrate that the predominant and substoichiometric arrangements of this IR have changed several times in other cupressophytes as well, providing compelling evidence for substoices shifting of plastomic forms during Cupressophyte evolution and suggest that substOichiometric shifting activity in plastid genomes may be adaptive.
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Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes
TLDR
It is demonstrated that M. conductrix is deeply nested within the Chlorella clade, suggesting that taxonomic revision is needed for one or both genera, and that the endosymbiotic lifestyle has evolved multiple times in Chlorellaceae.
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Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns.
TLDR
The first mitochondrial genomes of ferns show a mix of features shared with lycophytes and/or seed plants and several novel genomic features, enabling a robust reconstruction of the mitogenome in the common ancestor of vascular plants.
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High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants
TLDR
It is shown that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.
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Evolution of Plant Mitochondrial Intron-Encoded Maturases: Frequent Lineage-Specific Loss and Recurrent Intracellular Transfer to the Nucleus
TLDR
The findings indicate that plant mitochondrial maturases have experienced a surprisingly dynamic history due to a complex interaction of multiple evolutionary forces that affect the rates of maturase gain, retention, and loss.
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Extensive shifts from cis to trans splicing of gymnosperm mitochondrial introns.
TLDR
The prevalence of trans splicing in vascular plant lineages with recombinogenic mitogenomes suggests that genomic rearrangement is the primary cause of shifts from cis to trans splice in plant mitochondria.
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