The economics of organellar gene loss and endosymbiotic gene transfer

Kelly, Steven

doi:10.1101/2020.10.01.322487

Cited by 4 publications

(4 citation statements)

References 103 publications

(168 reference statements)

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“… Brandvain and Wade (2009) provides a model to explore the influence of population-genetic parameters (such as selection, dominance, mutation rates and population size with a rate of self-fertilization) on the rate and probability of functional gene transfer from mitochondrial genome (haploid) to nuclear genome (diploid). ( Kelly, 2020 ) defines an EGT simulation model based on the ATP biosynthesis cost for the encoding of a mitochondrial/chloroplast gene in the nuclear genome and the import of the resulting in the organelle. These prior works provide useful insights to design a model for the simulation of EGT evolutionary histories that would be strongly inspired from existing model for the simulation of HGT evolutionary histories.…”

Section: Discussionmentioning

confidence: 99%

Gene tree and species tree reconciliation with endosymbiotic gene transfer

et al. 2021

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Motivation It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α−proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree. Results We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees. Availability and implementation EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.

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Section: Discussionmentioning

confidence: 99%

Gene tree and species tree reconciliation with endosymbiotic gene transfer

et al. 2021

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“…This event is known to have played a major role in the evolution of eukaryotes [141,142]. Although prior work provides useful insights to understand the parameters influencing such an event [143,144], designing an appropriate model for the simulation of EGT evolutionary histories that can be used to assess the accuracy of our algorithm in [137] remains to be done.…”

Section: Discussionmentioning

confidence: 99%

Predicting the Evolution of Syntenies—An Algorithmic Review

El-Mabrouk

2021

Algorithms

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Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders, while more relaxed definitions just require a certain similarity in gene content, and not necessarily in the same order. Regardless of the way they are identified, the goal is to characterize homologous genomic regions, i.e., regions deriving from a common ancestral region, reflecting a certain gene co-evolution that can enlighten important functional properties. In addition of being able to identify them, it is also necessary to infer the evolutionary history that has led from the ancestral segment to the extant ones. In this field, most algorithmic studies address the problem of inferring rearrangement scenarios explaining the disruption in gene order between segments with the same gene content, some of them extending the evolutionary model to gene insertion and deletion. However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another. Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization to segmental events and to syntenies. This paper reviews some of the main algorithmic methods for inferring ancestral syntenies and focus on those integrating both gene orders and gene trees.

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“…Eukaryotes gained the capacity for photosynthesis ~1.5 billion years ago when a single celled eukaryotic organism engulfed a cyanobacterium (Schwartz and Dayhoff 1978;Martin and Kowallik 1999;Hedges, et al 2004). As the cyanobacterium evolved into the semiautonomous organelle known as the plastid, its genome underwent a substantial reduction, such that it now harbours <5% of the genes found in its cyanobacterial ancestor (Blanchard and Schmidt 1995;Martin, et al 2002;Kelly 2021). Despite this large reduction, the gene content and organisation has been highly conserved across the angiosperm lineage (Palmer and Thompson 1982;Jansen, et al 2007;Zhu, et al 2016;Robbins and Kelly 2023).…”

Section: Introductionmentioning

confidence: 99%

Widespread adaptive evolution in the photosystems of angiosperms provides new insight into the evolution of photosystem II repair

Robbins,

Kelly

2024

Preprint

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Oxygenic photosynthesis generates the initial energy source which fuels nearly all life on earth. At the heart of the process are the photosystems, pigment binding multi-protein complexes that catalyse the first step of photochemical conversion of light energy into chemical energy. Here, we investigate the molecular evolution at single residue resolution of the plastid-encoded subunits of the photosystems across 773 angiosperm species. We show that despite an extremely high level of conservation, 7% of residues in the photosystems, spanning all photosystem subunits, exhibit hallmarks of adaptive evolution. Through in silico modelling of these adaptive substitutions we uncover the impact of these changes on the properties of the photosystems, focussing on their effects on co-factor binding and the formation of inter-subunit interfaces. We further reveal that evolution has repeatedly destabilised the interaction photosystem II and its D1 subunit, thereby reducing the energetic barrier for D1 turn-over and photosystem repair. Together, these results provide new insight into the trajectory of photosystem evolution during the radiation of the angiosperms.

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The economics of organellar gene loss and endosymbiotic gene transfer

Cited by 4 publications

References 103 publications

Gene tree and species tree reconciliation with endosymbiotic gene transfer

Gene tree and species tree reconciliation with endosymbiotic gene transfer

Predicting the Evolution of Syntenies—An Algorithmic Review

Widespread adaptive evolution in the photosystems of angiosperms provides new insight into the evolution of photosystem II repair

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