Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification

Sevillya, Gur; Snir, Sagi

doi:10.1016/j.ympev.2019.03.010

Cited by 11 publications

(8 citation statements)

References 44 publications

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“…Synteny provides an alternative metric to gauge the unison of ptx-ptd gene evolution because 1) linked genes tend to maintain organization throughout evolutionary history, and 2) closely related taxa show high genomic stability (43,44). We found that the individual ptx and ptd genes were always codirectional in the order ptxED and ptdFC(G)HI, respectively (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 87%

The diversity and evolution of microbial dissimilatory phosphite oxidation

Ewens

Gomberg

Barnum

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (Eo′) of −650 mV for the PO43−/PO33− couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A. Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.

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Section: Resultsmentioning

confidence: 87%

The diversity and evolution of microbial dissimilatory phosphite oxidation

Ewens

Gomberg

Barnum

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…This is a follow-up work of [28] and [25], from an evolutionary point of view. Here, we analyse and compare between two evolutionary clocks.…”

Section: Discussionmentioning

confidence: 92%

“…In a previous paper [ 28 ], we defined

, to measure the linear ratio between point mutation process and genome rearrangement. In this study we dive into the depths of this relation.…”

Section: Resultsmentioning

confidence: 99%

“…We can, theoretically, place each pair of species somewhere along this line, according to the height of their last common ancestor (LCA) in the evolutionary tree. As demonstrated in our previous work [ 28 ], closely related species, i.e. pairs placed in the right-hand side of the evolutionary scale, are phylogenetically analysed better by the SI approach, while at some point on the evolutionary scale, SI comes to saturation and data is better analysed by a point mutation-based approach.…”

Section: Resultsmentioning

confidence: 99%

“…In order to cluster all eggNOG species into some groups of closely related species, we executed the following approach, as described in [ 28 ]. We aimed to find cliques of related species based on the SI distance matrix, i.e.…”

Section: Methodsmentioning

confidence: 99%

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Relation between two evolutionary clocks reveal new insights in bacterial evolution

Sevillya

2022

Access Microbiology

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New insights in evolution are available thanks to next-generation sequencing technologies in recent years. However, due to the network of complex relations between species, caused by the intensive horizontal gene transfer (HGT) between different bacterial species, it is difficult to discover bacterial evolution. This difficulty leads to new research in the field of phylogeny, including the gene-based phylogeny, in contrast to sequence-based phylogeny. In previous articles, we presented evolutionary insights of Synteny Index (SI) study on a large biological dataset. We showed that the SI approach naturally clusters 1133 species into 39 cliques of closely related species. In addition, we presented a model that enables calculation of the number of translocation events between genomes based on their SI distance. Here, these two studies are combined together and lead to new insights. A principal result is the relation between two evolutionary clocks: the well-known sequence-based clock influenced by point mutations, and SI distance clock influenced by translocation events. A surprising linear relation between these two evolutionary clocks rising for closely related species across all genus. In other words, these two different clocks are ticking at the same rate inside the genus level. Conversely, a phase-transition manner discovered between these two clocks across non-closely related species. This may suggest a new genus definition based on an analytic approach, since the phase-transition occurs where each gene, on average, undergoes one translocation event. In addition, rare cases of HGT among highly conserved genes can be detected as outliers from the phase-transition pattern.

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