scholarly journals Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages

Algorithms ◽  
2021 ◽  
Vol 14 (8) ◽  
pp. 231
Author(s):  
Samson Weiner ◽  
Mukul S. Bansal
Keyword(s):  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Computational Technique ◽  
Transfer Event ◽  
Extinct Species ◽  
Reconciliation Analysis ◽  
Evolution Of Gene Families ◽  
The Impact

Duplication-Transfer-Loss (DTL) reconciliation is a widely used computational technique for understanding gene family evolution and inferring horizontal gene transfer (transfer for short) in microbes. However, most existing models and implementations of DTL reconciliation cannot account for the effect of unsampled or extinct species lineages on the evolution of gene families, likely affecting their accuracy. Accounting for the presence and possible impact of any unsampled species lineages, including those that are extinct, is especially important for inferring and studying horizontal transfer since many genes in the species lineages represented in the reconciliation analysis are likely to have been acquired through horizontal transfer from unsampled lineages. While models of DTL reconciliation that account for transfer from unsampled lineages have already been proposed, they use a relatively simple framework for transfer from unsampled lineages and cannot explicitly infer the location on the species tree of each unsampled or extinct lineage associated with an identified transfer event. Furthermore, there does not yet exist any systematic studies to assess the impact of accounting for unsampled lineages on the accuracy of DTL reconciliation. In this work, we address these deficiencies by (i) introducing an extended DTL reconciliation model, called the DTLx reconciliation model, that accounts for unsampled and extinct species lineages in a new, more functional manner compared to existing models, (ii) showing that optimal reconciliations under the new DTLx reconciliation model can be computed just as efficiently as under the fastest DTL reconciliation model, (iii) providing an efficient algorithm for sampling optimal DTLx reconciliations uniformly at random, (iv) performing the first systematic simulation study to assess the impact of accounting for unsampled lineages on the accuracy of DTL reconciliation, and (v) comparing the accuracies of inferring transfers from unsampled lineages under our new model and the only other previously proposed parsimony-based model for this problem.

scholarly journals Extensive Phenotypic Changes Associated with Large-scale Horizontal Gene Transfer

2013 ◽  
Author(s):  
Kevin Dougherty ◽  
Brian A Smith ◽  
Autum F Moore ◽  
Shannon Maitland ◽  
Chris Fanger ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Pseudomonas Stutzeri ◽  
Transfer Event ◽  
Small Plasmid ◽  
Phenotypic Changes ◽  
Evolutionary Trajectories ◽  
Evolutionary Consequences

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e. changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmid and phage, little is known about how size of the acquired region affects the magnitude or number of such costs. Here we describe an amazing breadth of phenotypic changes which occur after a large-scale horizontal transfer event (~1Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.

scholarly journals Horizontal transfer of the n-TASE gene cluster in Burkholderia seminalis TC3.4.2R3 inferred from phylogenetic and molecular methods

2021 ◽  
Author(s):  
Sarina Tsui ◽  
Welington Luiz Araújo
Keyword(s):  
Comparative Genomics ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Horizontal Gene Transfer Event ◽  
Donor Strain ◽  
Biotechnological Applications ◽  
Transfer Event ◽  
Species Phylogeny ◽  
Homologous Genes

Abstract This study describes the n-TASE cluster in Burkholderia seminalis TC3.4.2R3, which was present in B. contaminans (CP046609.1), but absent in other related Burkholderia species. Phylogeny, comparative genomics and molecular analysis indicated it is not common to B. seminalis species, presenting similarity with homologous genes presents Aquamicrobium sp. SK-2 and B. contaminans LMG23361, probably acquired by an HGT (Horizontal Gene Transfer) event. It was not possible to determine which was the most likely donor strain of the n-TASE cluster. The HGT event did not occur in all strains of the Bcc group, nor in the B. seminalis, but it did occur punctually in the strain B. seminalis TC34.2R3. It has a correlation in biotechnological applications related processes. Aiming at understanding the involvement of the n-TASE cluster in the interaction of this bacterium in the environment, genes in this cluster will be inactivated, next.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

Biodynamic Modeling of a Pedestrian Impact With a Rigid Frontal Guard of a Utility Vehicle

2010 ◽  
Author(s):  
Rasoul Moradi ◽  
Chandrashekhar K. Thorbole ◽  
Michael McCoy ◽  
Hamid M. Lankarani
Keyword(s):  
Front Surface ◽  
Body Region ◽  
Computational Technique ◽  
Surface Model ◽  
Published Data ◽  
Factors Affecting ◽  
Light Trucks ◽  
Accident Data ◽  
Facet Surface ◽  
The Impact

Accident data reveals that in most pedestrian accidents, the pedestrian head and lower extremity are vulnerable to serious injuries. The vehicle front geometry profile as well as the impact speed are important factors affecting the pedestrian kinematics and injury potential. In the US, accident data also shows that the fatality rate for pedestrian/light trucks and vans (LTV) impact is greater than that for the pedestrian/passenger-car impact. Addition of a front guard on light trucks and sports utility vehicles to mitigate damage during off-road activity or to provide mounting points for extra lights, makes the pedestrian more vulnerable to the impact. In this paper, a computational technique is utilized to study the influence of the added front guard on the impacted pedestrian. A CAD model of a typical commercial frontal guard is developed and converted into a rigid facet model, and attached to the vehicle front. The validated standing dummy model in the MADYMO code is used to simulate a pedestrian, and the rigid facet-surface model of a pickup truck is used to generate a vehicle front surface. This computational model is validated by comparing the pedestrian kinematics with the published data. This study demonstrates that the pedestrian mid body region is more vulnerable with the addition of guard on the vehicle. The result from this study facilitates a better understanding of a guard design and its geometry profile as required to protect vulnerable road users.

scholarly journals Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei

2021 ◽  
Author(s):  
Kim Vertacnik ◽  
Danielle Herrig ◽  
R Keating Godfrey ◽  
Tom Hill ◽  
Scott Geib ◽  
...  
Keyword(s):  
Gene Family ◽  
Family Size ◽  
Draft Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Gene Gain ◽  
Ecological Specialization ◽  
Dietary Specialization ◽  
Pine Sawfly ◽  
Neodiprion Lecontei

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions and characterized their genomic distributions and evolutionary history. Our results suggest that expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), and antimicrobial peptide (AMP) subfamilies may have contributed to pine adaptation. By contrast, there was no evidence of recent gene family contraction via pseudogenization. Next, we compared the number of genes in these same families across insect taxa that vary in diet, dietary specialization, and social behavior. In Hymenoptera, herbivory was associated with large GR and small olfactory receptor (OR) families, eusociality was associated with large OR and small AMP families, and--unlike investigations among more closely related taxa--ecological specialization was not related to gene family size. Overall, our results suggest that gene families that mediate ecological interactions may expand and contract predictably in response to particular selection pressures, however, the ecological drivers and temporal pace of gene gain and loss likely varies considerably across gene families.

scholarly journals treeWidget: a BioJS component to visualise phylogenetic trees

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 49 ◽  
Author(s):  
Fabian Schreiber
Keyword(s):  
Phylogenetic Trees ◽  
Protein Domains ◽  
Gene Families ◽  
Sequence Information ◽  
Gene Duplications ◽  
Link Type ◽  
History Of ◽  
Conservation Patterns ◽  
Evolution Of Gene Families ◽  
The Web

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707

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