Detecting horizontal gene transfer: a probabilistic approach

Sevillya, Gur; Adato, Orit; Snir, Sagi

doi:10.1186/s12864-019-6395-5

Cited by 23 publications

(15 citation statements)

References 30 publications

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“…There are three possible scenarios leading to detectable signals in biological data. First, HR and HGT affect the relative positions of genes in the genome through loci gain/loss, repositioning, and duplication, thus, disrupting synteny which is especially conspicuous when comparing whole-genome sequences from diverse strains [ 49 , 50 ]. Second, phylogeny reconstruction based on different loci susceptible to HR or stemming from HGT would cause inconsistencies when collating different gene-based trees or comparing them to those representing species evolution [ 1 , 2 ].…”

Section: A Brief Overview Of Conventional Methods For Detecting Homol...mentioning

confidence: 99%

“…In the end, the chi-square test is performed to calculate the significance of the predicted events [ 49 ]. A further improvement considers the length of the transfer genes and also utilizes the Chernoff bound test instead of the chi-square test, thus, reducing the number of false-positive calls [ 50 ]. The nearHGT program has been applied to evaluate the HGT rate in Mycobacterium leprae , which displayed that pseudogenized loci were transferred with increased frequency in contrast to functional genes [ 9 ].…”

Section: Current Bioinformatics Tools For Recombination Analysismentioning

confidence: 99%

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Current Methods for Recombination Detection in Bacteria

Shikov

Malovichko

Nizhnikov

et al. 2022

IJMS

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The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of software. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic approaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.

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Section: A Brief Overview Of Conventional Methods For Detecting Homol...mentioning

confidence: 99%

Section: Current Bioinformatics Tools For Recombination Analysismentioning

confidence: 99%

Current Methods for Recombination Detection in Bacteria

Shikov

Malovichko

Nizhnikov

et al. 2022

IJMS

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“…We investigated the potential evolutionary origin of these putative IBPs by selecting a strong IBP match in a search organism, Mytilus coruscus, with many closely related species with genomic resources to be treated as a proof of principle. A basic search for synteny proved fruitless in this study, which can be used as support for horizontal gene transfer (Sevillya et al, 2020). However, for reasons mentioned above, we believe that this IBP evolved convergently and horizontal gene transfer could not be responsible for the acquisition of this protein.…”

Section: Discussionmentioning

confidence: 78%

Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates

Box

Matthews

Marshall

2021

Preprint

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Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival of sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more ice-binding proteins than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an ice-binding protein was significantly greater in intertidal species as compared to those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk, that there is an array of uncharacterized ice binding proteins and highlight the need for broader laboratory-based surveys of the diversity of ice binding activity across diverse taxonomic and ecological groups.Summary statementIntertidal invertebrates have a disproportionate number of putative ice-binding proteins relative to other habitats. These putative proteins are highly similar to antifreeze glycoproteins and type II antifreeze proteins from fish.

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“…We investigated the potential evolutionary origin of these putative IBPs by selecting a strong IBP match in a search organism, M. coruscus, with many closely related species with genomic resources to be treated as a proof of principle. A basic search for synteny proved fruitless in this study, which can be used as support for horizontal gene transfer (Sevillya et al, 2020). However, for reasons mentioned above, we believe that this putative IBP evolved convergently and horizontal gene transfer could not be responsible for the acquisition of this protein.…”

Section: Evolutionmentioning

confidence: 77%

Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates

Box

Matthews

Marshall

2022

Journal of Experimental Biology

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Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival at sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more IBPs than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an IBP was significantly greater in intertidal species than in those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk and that there is an array of uncharacterized IBPs, and highlight the need for broader laboratory-based surveys of the diversity of ice-binding activity across diverse taxonomic and ecological groups.

show abstract

Detecting horizontal gene transfer: a probabilistic approach

Cited by 23 publications

References 30 publications

Current Methods for Recombination Detection in Bacteria

Current Methods for Recombination Detection in Bacteria

Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates

Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates

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