Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes

Tria, Fernando D. K.; Martin, William

doi:10.1093/gbe/evab224

Cited by 27 publications

(45 citation statements)

References 54 publications

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“…The remaining five roots identified with a T:D of 50:1 fell within the bacterial group that Coleman et al [17] designate as Gracilicutes (Figure 1). In an earlier study focusing on recent gene transfers and recent gene duplications, we found that average bacterial T:D ratios across genes can approach or exceed 100:1 in some bacterial lineages [22]. To understand what influence a higher T:D ratio would have on the root inferences, we repeated the tests by setting T and D across gene trees so as to conform to a 100:1 T:D ratio.…”

Section: Gene Transfer To Gene Duplication Ratios Constrain the Numbe...mentioning

confidence: 99%

Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method

Bremer

Knopp

Martin

et al. 2022

Life

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The rooting of phylogenetic trees permits important inferences about ancestral states and the polarity of evolutionary events. Recently, methods that reconcile discordance between gene-trees and species-trees—tree reconciliation methods—are becoming increasingly popular for rooting species trees. Rooting via reconciliation requires values for a particular parameter, the gene transfer to gene duplication ratio (T:D), which in current practice is estimated on the fly from discordances observed in the trees. To date, the accuracy of T:D estimates obtained by reconciliation analyses has not been compared to T:D estimates obtained by independent means, hence the effect of T:D upon inferences of species tree roots is altogether unexplored. Here we investigated the issue in detail by performing tree reconciliations of more than 10,000 gene trees under a variety of T:D ratios for two phylogenetic cases: a bacterial (prokaryotic) tree with 265 species and a fungal-metazoan (eukaryotic) tree with 31 species. We show that the T:D ratios automatically estimated by a current tree reconciliation method, ALE, generate virtually identical T:D ratios across bacterial genes and fungal-metazoan genes. The T:D ratios estimated by ALE differ 10- to 100-fold from robust, ALE-independent estimates from real data. More important is our finding that the root inferences using ALE in both datasets are strongly dependent upon T:D. Using more realistic T:D ratios, the number of roots inferred by ALE consistently increases and, in some cases, clearly incorrect roots are inferred. Furthermore, our analyses reveal that gene duplications have a far greater impact on ALE’s preferences for phylogenetic root placement than gene transfers or gene losses do. Overall, we show that obtaining reliable species tree roots with ALE is only possible when gene duplications are abundant in the data and the number of falsely inferred gene duplications is low. Finding a sufficient sample of true gene duplications for rooting species trees critically depends on the T:D ratios used in the analyses. T:D ratios, while being important parameters of genome evolution in their own right, affect the root inferences with tree reconciliations to an unanticipated degree.

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Section: Gene Transfer To Gene Duplication Ratios Constrain the Numbe...mentioning

confidence: 99%

Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method

Bremer

Knopp

Martin

et al. 2022

Life

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“…Rate estimation is, however, challenging and the impact of incorrect rates on the accuracy of species tree rooting with reconciliation models is currently unknown. Indeed, evolutionary rates as estimated by tree reconciliation analyses often contradict more conservative estimates obtained by independent studies (Treangen and Rocha 2011;Tria and Martin 2021), indicating possible biases within reconciliation models. By contrast, the rooting approach presented here does not rely on a priori estimates of evolutionary rates and, as such, offer a simpler solution to the species root problem in comparison to tree reconciliation approaches.…”

Section: Discussionmentioning

confidence: 90%

Phylogenomic Testing of Root Hypotheses

Tria

Landan

2019

Preprint

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17The determination of the last common ancestor (LCA) of a group of species plays a 18 vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully 19 resolved species tree. From a theoretical perspective, however, inference of the LCA 20 amounts to the reconstruction of just one branch -the root branch -of the true unrooted 21 species tree, and should therefore be a much easier task than the full resolution of the 22 a chemolithoautotrophic and anaerobic life-style. Our inference is based on data comprising 33 between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching 34 LCA inference within a statistical framework thus renders the phylogenomic inference 35 powerful and robust. 36 37

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“…Genes (and proteins by extension) are known to evolve from gene duplication, gene transfer and mutation events. Compared to these two occurrences, gene insertions are rare (29)(30)(31). Therefore, classifying sequences based on their phylum of origin can help obtain candidates that have undergone a gradual change in the line of evolution and speciation.…”

Section: Resultsmentioning

confidence: 99%

Flexibility of Short-chain dehydrogenase is interconnected to its promiscuity for the reduction of multiple ketone intermediates

Shanbhag

Rajagopal

Katagihallimath

et al. 2021

Preprint

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Short-chain dehydrogenases/reductases (SDRs) are an essential family of enzymes used to synthesize enantiopure alcohols. Several studies describe prospected or engineered candidates for converting substrates of interest using cost and time-intensive high-throughput approaches. For catalysis, SDRs are classified into five types based on chain length and cofactor binding site. Of these, the shorter Classical and the longer Extended enzymes participate in ketoreduction. However, comparative analysis of various modelled SDRs reveals a length independent conserved N-terminal Rossmann fold and a variable C-terminus region. The latter domain is hypothesized to affect the flexibility of the enzyme. We have used machine learning on this flexible domain to build a rationale to screen promiscuous SDRs. A dataset consisting of physicochemical properties derived from the amino-acid composition of enzymes is used to select closely associated promiscuous mesophilic enzymes. The resulting in vitro studies on pro-pharmaceutical substrates illustrate a direct correlation between the C-terminal lid-loop structure, enzyme melting temperature and the turnover number. We present a walkthrough for exploring promiscuous SDRs for catalyzing enantiopure alcohols of industrial importance.

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Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes

Cited by 27 publications

References 54 publications

Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method

Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method

Phylogenomic Testing of Root Hypotheses

Flexibility of Short-chain dehydrogenase is interconnected to its promiscuity for the reduction of multiple ketone intermediates

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