The mutational hazard hypothesis of organelle genome evolution: 10 years on

Smith, David Roy

doi:10.1111/mec.13742

Cited by 50 publications

(57 citation statements)

References 56 publications

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“…2012). Although a handful of exceptions have been noted, the effect of random genetic drift and mutation rates gives an alternative explanation for organelle genomic evolution (Smith 2016). …”

Section: Introductionmentioning

confidence: 99%

Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)

Chaw

2016

Genome Biol Evol

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Conifers II (cupressophytes), comprising about 400 tree species in five families, are the most diverse group of living gymnosperms. Their plastid genomes (plastomes) are highly variable in size and organization, but such variation has never been systematically studied. In this study, we assessed the potential mechanisms underlying the evolution of cupressophyte plastomes. We analyzed the plastomes of 24 representative genera in all of the five cupressophyte families, focusing on their variation in size, noncoding DNA content, and nucleotide substitution rates. Using a tree-based method, we further inferred the ancestral plastomic organizations of internal nodes and evaluated the inversions across the evolutionary history of cupressophytes. Our data showed that variation in plastome size is statistically associated with the dynamics of noncoding DNA content, which results in different degrees of plastomic compactness among the cupressophyte families. The degrees of plastomic inversions also vary among the families, with the number of inversions per genus ranging from 0 in Araucariaceae to 1.27 in Cupressaceae. In addition, we demonstrated that synonymous substitution rates are significantly correlated with plastome size as well as degree of inversions. These data suggest that in cupressophytes, mutation rates play a critical role in driving the evolution of plastomic size while plastomic inversions evolve in a neutral manner.

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Section: Introductionmentioning

confidence: 99%

Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)

Chaw

2016

Genome Biol Evol

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“…Figure 1 shown that 5' splicing signal, the polypyrimidine tract and 3' splicing signal of introns from left to right. We found that the consensus signals of the introns of the carnivorous plants were similar to those of eukaryotes, like land plants, metazoan and mammals (Irimia and Roy, 2008;Ma et al, 2015a;2016).…”

Section: Intron Consensus Sequence In the Carnivorous Plantsmentioning

confidence: 73%

“…By comparing the nuclear genomes and organellar genomes, Lynch found a large number of introns accumulation in the nuclear genome and he believes that it is due to differences in the mutation rates between the two genomic groups. Meanwhile, he also found that the complexity of the organelle genome was significantly reduced, supporting the mutationalhazard hypothesis Smith, 2016).…”

Section: Introductionmentioning

confidence: 73%

The Evolution Force of Genome Reduction in Carnivorous Plants

Ma¹,

Tan²,

Yin³

et al. 2018

American Journal of Biochemistry and Biotechnology

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Abstract:The introns are widely present in the genome of eukaryotes and the distribution of intron varies greatly among different organisms or different genes. Generally, introns loss is an important way for uneven distribution of intron during genome evolution. In this study, two closely related carnivorous plants (Genlisea aurea and Utricularia gibba) were chosen, their genome were relatively integrity and high quality, especially, the large difference in genome size between them. We detected intron loss events, then investigated the relationship between the genome size, intron density, intron loss and the mutation rate in the carnivorous plants. Finally, a total of 752 and 124 intron loss positions were identified in G. aurea and U. gibba, respectively. In carnivorous plants, we found that the region around lost site had high mutation rate, the genes of intron loss had high mutation rate. Besides, for the species with more intron losses, the genome size was smaller and the mutation rate was higher. Thus, we propose that the mutation rate was positively correlated with intron losses, but negatively correlated with intron number and genome size. These could be explained by the selection to minimize mutational hazards.

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“…The roots of organelle genomic expansion are complicated and multifaceted (Smith, 2016). There is increasing evidence that DNA maintenance machineries play a key role in organelle genomic architecture, including genome size (Smith and Keeling, 2015).…”

Section: Ptdna-coding Capacity Is Highly Conserved Among Colorless Algaementioning

confidence: 99%

The Plastid Genome of Polytoma uvella Is the Largest Known among Colorless Algae and Plants and Reflects Contrasting Evolutionary Paths to Nonphotosynthetic Lifestyles

et al. 2016

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The loss of photosynthesis is frequently associated with parasitic or pathogenic lifestyles, but it also can occur in free-living, plastid-bearing lineages. A common consequence of becoming nonphotosynthetic is the reduction in size and gene content of the plastid genome. In exceptional circumstances, it can even result in the complete loss of the plastid DNA (ptDNA) and its associated gene expression system, as reported recently in several lineages, including the nonphotosynthetic green algal genus Polytomella. Closely related to Polytomella is the polyphyletic genus Polytoma, the members of which lost photosynthesis independently of Polytomella. Species from both genera are free-living organisms that contain nonphotosynthetic plastids, but unlike Polytomella, Polytoma members have retained a genome in their colorless plastid. Here, we present the plastid genome of Polytoma uvella: to our knowledge, the first report of ptDNA from a nonphotosynthetic chlamydomonadalean alga. The P. uvella ptDNA contains 25 protein-coding genes, most of which are related to gene expression and none are connected to photosynthesis. However, despite its reduced coding capacity, the P. uvella ptDNA is inflated with short repeats and is tens of kilobases larger than the ptDNAs of its closest known photosynthetic relatives, Chlamydomonas leiostraca and Chlamydomonas applanata. In fact, at approximately 230 kb, the ptDNA of P. uvella represents the largest plastid genome currently reported from a nonphotosynthetic alga or plant. Overall, the P. uvella and Polytomella plastid genomes reveal two very different evolutionary paths following the loss of photosynthesis: expansion and complete deletion, respectively. We hypothesize that recombination-based DNA-repair mechanisms are at least partially responsible for the different evolutionary outcomes observed in such closely related nonphotosynthetic algae.

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The mutational hazard hypothesis of organelle genome evolution: 10 years on

Cited by 50 publications

References 56 publications

Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)

Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)

The Evolution Force of Genome Reduction in Carnivorous Plants

The Plastid Genome of Polytoma uvella Is the Largest Known among Colorless Algae and Plants and Reflects Contrasting Evolutionary Paths to Nonphotosynthetic Lifestyles

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