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Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates.
- Andan Zhu, Wenhu Guo, Sakshi Gupta, Weishu Fan, Jeffrey P. Mower
- BiologyThe New phytologist
- 1 March 2016
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.
Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution.
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.
Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution
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.
Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes
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.
Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns.
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.
Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae
Results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.
Extensive shifts from cis to trans splicing of gymnosperm mitochondrial introns.
- Wenhu Guo, Andan Zhu, Weishu Fan, R. P. Adams, Jeffrey P. Mower
- BiologyMolecular biology and evolution
- 6 February 2020
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.
Phylogenomic evidence for ancient recombination between plastid genomes of the Cupressus-Juniperus-Xanthocyparis complex (Cupressaceae)
- Andan Zhu, Weishu Fan, R. P. Adams, Jeffrey P. Mower
- BiologyBMC Evolutionary Biology
- 10 September 2018
It is suggested that the conflicting plastomic signals result from an ancient introgression event involving ycf1 and ycf2 that occurred in an ancestor of this species complex, offering further evidence that recombination occurs between plastomes.
Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella.
Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis
- Weishu Fan, Wenhu Guo, L. Funk, Jeffrey P. Mower, Andan Zhu
- BiologyScience China Life Sciences
- 7 March 2019
This result is the first study to uncover massive editing loss from both the mitogenome and plastome in a single genus and suggests that gene expression level and retroprocessing both contributed to the evolution of RNA editing in plant organellar genomes.