scholarly journals Phylogenetic reconstruction based on synteny block and gene adjacencies

2019 ◽  
Author(s):  
Guénola Drillon ◽  
Raphaël Champeimont ◽  
Francesco Oteri ◽  
Gilles Fischer ◽  
Alessandra Carbone
Keyword(s):  
Chromosomal Rearrangements ◽  
Phylogenetic Reconstruction ◽  
Simulated Data ◽  
Synteny Block ◽  
Reconstruction Method ◽  
Reconstruction Methods ◽  
Wide Range ◽  
Genomic Markers ◽  
Tree Topologies ◽  
Almost All

AbstractGene order can be used as an informative character to reconstruct phylogenetic relationships-between species independently from the local information present in gene/protein sequences.PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches.PhyChro performance isevaluatedon two datasets of 13 vertebrates and 21 yeast genomes by using up to 130 000 and 179 000 breakpoints respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared to other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in less than 15 min.AvailabilityPhyChro will be freely available under the BSD license after [email protected]

scholarly journals Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

2020 ◽  
Vol 37 (9) ◽  
pp. 2747-2762 ◽  
Author(s):  
Guénola Drillon ◽  
Raphaël Champeimont ◽  
Francesco Oteri ◽  
Gilles Fischer ◽  
Alessandra Carbone
Keyword(s):  
Chromosomal Rearrangements ◽  
Phylogenetic Reconstruction ◽  
Simulated Data ◽  
Synteny Block ◽  
Data Sets ◽  
Reconstruction Method ◽  
Reconstruction Methods ◽  
Wide Range ◽  
Genomic Markers ◽  
Almost All

Abstract Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively, supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches. PhyChro performance is evaluated on two data sets of 13 vertebrates and 21 yeast genomes by using up to 130,000 and 179,000 breakpoints, respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared with other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in <15 min.

scholarly journals Ultra-fast accurate reconstruction of spiking activity from calcium imaging data

2018 ◽  
Vol 119 (5) ◽  
pp. 1863-1878 ◽  
Author(s):  
Vahid Rahmati ◽  
Knut Kirmse ◽  
Knut Holthoff ◽  
Stefan J. Kiebel
Keyword(s):  
Calcium Imaging ◽  
Reconstruction Method ◽  
Imaging Data ◽  
Decay Kinetics ◽  
Experimental Conditions ◽  
Model Free ◽  
Reconstruction Methods ◽  
Wide Range ◽  
Fast Processing ◽  
Spiking Activity

Calcium imaging provides an indirect observation of the underlying neural dynamics and enables the functional analysis of neuronal populations. However, the recorded fluorescence traces are temporally smeared, thus making the reconstruction of exact spiking activity challenging. Most of the established methods to tackle this issue are limited in dealing with issues such as the variability in the kinetics of fluorescence transients, fast processing of long-term data, high firing rates, and measurement noise. We propose a novel, heuristic reconstruction method to overcome these limitations. By using both synthetic and experimental data, we demonstrate the four main features of this method: 1) it accurately reconstructs both isolated spikes and within-burst spikes, and the spike count per fluorescence transient, from a given noisy fluorescence trace; 2) it performs the reconstruction of a trace extracted from 1,000,000 frames in less than 2 s; 3) it adapts to transients with different rise and decay kinetics or amplitudes, both within and across single neurons; and 4) it has only one key parameter, which we will show can be set in a nearly automatic way to an approximately optimal value. Furthermore, we demonstrate the ability of the method to effectively correct for fast and rather complex, slowly varying drifts as frequently observed in in vivo data. NEW & NOTEWORTHY Reconstruction of spiking activities from calcium imaging data remains challenging. Most of the established reconstruction methods not only have limitations in adapting to systematic variations in the data and fast processing of large amounts of data, but their results also depend on the user’s experience. To overcome these limitations, we present a novel, heuristic model-free-type method that enables an ultra-fast, accurate, near-automatic reconstruction from data recorded under a wide range of experimental conditions.

scholarly journals Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

2018 ◽  
Vol 3 ◽  
pp. 33 ◽  
Author(s):  
John A. Lees ◽  
Michelle Kendall ◽  
Julian Parkhill ◽  
Caroline Colijn ◽  
Stephen D. Bentley ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Reconstruction ◽  
Simulated Data ◽  
Real Data ◽  
Tree Topology ◽  
Computational Time ◽  
Advantages And Disadvantages ◽  
Phylogenetic Reconstructions ◽  
Reconstruction Methods ◽  
True Tree

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined 'true tree' using a realistic evolutionary model. We  built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. For the most accurate tree, use of either RAxML or IQ-TREE with an alignment of variable sites produced by mapping to a reference genome is best. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology.  We have publicly released our simulated data and code to enable further comparisons.

scholarly journals Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees

2016 ◽  
Vol 33 (10) ◽  
pp. 2720-2734 ◽  
Author(s):  
Prabhav Kalaghatgi ◽  
Nico Pfeifer ◽  
Thomas Lengauer
Keyword(s):  
Simulated Data ◽  
Information Criterion ◽  
Bootstrap Support ◽  
Evolutionary Relationships ◽  
Distance Threshold ◽  
Labeled Trees ◽  
Wide Range ◽  
Branching Points ◽  
Cross Validation Error ◽  
Almost All

Abstract The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct ancestral relationship, or if there is not enough information to fully resolve all the branching points in the evolutionary tree. In this article, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally labeled trees in which taxa may be placed at internal vertices and the tree may contain polytomies. FJ constructs such trees on the basis of pairwise distances and a distance threshold. We tested three methods for threshold selection, FJ-AIC, FJ-BIC, and FJ-CV, which minimize Akaike information criterion, Bayesian information criterion, and cross-validation error, respectively. When compared with related methods on simulated data, FJ-BIC was among the best at reconstructing the correct tree across a wide range of simulation scenarios. FJ-BIC was applied to HIV sequences sampled from individuals involved in a known transmission chain. The FJ-BIC tree was found to be compatible with almost all transmission events. On average, internal branches in the FJ-BIC tree have higher bootstrap support than branches in the leaf-labeled bifurcating tree constructed using RAxML. 36% and 25% of the internal branches in the FJ-BIC tree and RAxML tree, respectively, have bootstrap support greater than 70%. To the best of our knowledge the method presented here is the first attempt at modeling evolutionary relationships using generally labeled trees.

scholarly journals Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

2018 ◽  
Vol 3 ◽  
pp. 33 ◽  
Author(s):  
John A. Lees ◽  
Michelle Kendall ◽  
Julian Parkhill ◽  
Caroline Colijn ◽  
Stephen D. Bentley ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Reconstruction ◽  
Simulated Data ◽  
Real Data ◽  
Tree Topology ◽  
Computational Time ◽  
Advantages And Disadvantages ◽  
Phylogenetic Reconstructions ◽  
Reconstruction Methods ◽  
True Tree

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

scholarly journals A Robust Phylogeny of the Oropendolas: Polyphyly Revealed by Mitochondrial Sequence Data

The Auk ◽  
2002 ◽  
Vol 119 (2) ◽  
pp. 335-348 ◽  
Author(s):  
J. Jordan Price ◽  
Scott M. Lanyon
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Species Level ◽  
Species Relationships ◽  
Base Pairs ◽  
Phylogenetic Information ◽  
Multiple Exemplars ◽  
Reconstruction Methods ◽  
Mitochondrial Cytochrome B ◽  
Wide Range

Abstract We present a robust, fully resolved phylogeny for the oropendolas that will serve as a basis for comparative studies in this group. We sequenced 2,011 base pairs (bp) of the mitochondrial cytochrome-b and ND2 genes from 22 individuals to reconstruct relationships between recognized species and subspecies and to assess variation within polytypic taxa. A single phylogenetic tree was produced despite the use of a wide range of weighting schemes and phylogenetic reconstruction methods. Our data provide strong evidence that oropendolas are polyphyletic, with two distinct groups within a larger clade of oropendolas and caciques. We confirm the monophyly of recognized species, but indicate that some within-species relationships do not conform to recognized subspecies limits. Our findings thus demonstrate the importance of including multiple exemplars from each taxon of interest. The two genes provided complimentary and equally effective phylogenetic information for comparisons within the oropendolas, but exhibited lower resolution in comparisons above the species level.

First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon

2020 ◽  
Vol 20 ◽  
Author(s):  
Rami Obeid ◽  
Elias Wehbe ◽  
Mohamad Rima ◽  
Mohammad Kabara ◽  
Romeo Al Bersaoui ◽  
...  
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Viral Genome ◽  
Virus Genome ◽  
Enzyme Linked Immunosorbent Assay ◽  
Virus Family ◽  
Crop Fields ◽  
Wide Range ◽  
Almost All ◽  
Das Elisa

Background: Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particularly tobacco, causing a production loss. Objectives: Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon. Methods: Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crops samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome. Results and Discussion: PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain. Conclusion: Our study is the first in Lebanon revealing TMV infection in crop fields, and highlighting the danger that may affect the future of agriculture.

Cerebellotrigeminal Dermal Dysplasia (Gómez-López-Hernández Syndrome)

2018 ◽  
Vol 16 (05) ◽  
pp. 362-368 ◽  
Author(s):  
Federica Sullo ◽  
Agata Polizzi ◽  
Stefano Catanzaro ◽  
Selene Mantegna ◽  
Francesco Lacarrubba ◽  
...  
Keyword(s):  
De Novo ◽  
Chromosomal Rearrangements ◽  
Number Of Patients ◽  
Wide Range ◽  
Visual Problems ◽  
Neurodevelopmental Abnormalities ◽  
Clinical Triad ◽  
High Degree ◽  
Motor Handicap

Cerebellotrigeminal dermal (CTD) dysplasia is a rare neurocutaneous disorder characterized by a triad of symptoms: bilateral parieto-occipital alopecia, facial anesthesia in the trigeminal area, and rhombencephalosynapsis (RES), confirmed by cranial magnetic resonance imaging. CTD dysplasia is also known as Gómez-López-Hernández syndrome. So far, only 35 cases have been described with varying symptomatology. The etiology remains unknown. Either spontaneous dominant mutations or de novo chromosomal rearrangements have been proposed as possible explanations. In addition to its clinical triad of RES, parietal alopecia, and trigeminal anesthesia, CTD dysplasia is associated with a wide range of phenotypic and neurodevelopmental abnormalities.Treatment is symptomatic and includes physical rehabilitation, special education, dental care, and ocular protection against self-induced corneal trauma that causes ulcers and, later, corneal opacification. The prognosis is correlated to the mental development, motor handicap, corneal–facial anesthesia, and visual problems. Follow-up on a large number of patients with CTD dysplasia has never been reported and experience is limited to few cases to date. High degree of suspicion in a child presenting with characteristic alopecia and RES has a great importance in diagnosis of this syndrome.

INFLUENCE OF WEATHER ON TEMPORARY AND PERMANENT MIGRATION IN RURAL INDIA

2013 ◽  
Vol 04 (02) ◽  
pp. 1350007 ◽  
Author(s):  
K. S. KAVI KUMAR ◽  
BRINDA VISWANATHAN
Keyword(s):  
National Sample ◽  
Sample Survey ◽  
Urban Migration ◽  
Temporary Migration ◽  
Urban Migrants ◽  
Wide Range ◽  
Permanent Migration ◽  
Sample Survey Data ◽  
Almost All ◽  
Temporary Migrants

While a wide range of factors influence rural–rural and rural–urban migration in developing countries, there is significant interest in analyzing the role of agricultural distress and growing inter-regional differences in fueling such movement. This strand of research acquires importance in the context of climate change adaptation. In the Indian context, this analysis gets further complicated due to the significant presence of temporary migration. This paper analyzes how weather and its variability affects both temporary and permanent migration in India using National Sample Survey data for the year 2007–2008. The paper finds that almost all of the rural–urban migrants are permanent. Only temperature plays a role in permanent migration. In contrast, many temporary migrants are rural–rural and both temperature and rainfall explain temporary migration.

scholarly journals Nuclear Envelope Integrity in Health and Disease: Consequences on Genome Instability and Inflammation

2021 ◽  
Vol 22 (14) ◽  
pp. 7281
Author(s):  
Benoit R. Gauthier ◽  
Valentine Comaills
Keyword(s):  
Nuclear Envelope ◽  
Clinical Symptoms ◽  
Genome Instability ◽  
Chromosomal Rearrangements ◽  
Wide Range ◽  
Complex Chromosomal Rearrangements ◽  
Health And Disease ◽  
Dna Release ◽  
Sting Pathway ◽  
Eukaryote Genome

The dynamic nature of the nuclear envelope (NE) is often underestimated. The NE protects, regulates, and organizes the eukaryote genome and adapts to epigenetic changes and to its environment. The NE morphology is characterized by a wide range of diversity and abnormality such as invagination and blebbing, and it is a diagnostic factor for pathologies such as cancer. Recently, the micronuclei, a small nucleus that contains a full chromosome or a fragment thereof, has gained much attention. The NE of micronuclei is prone to collapse, leading to DNA release into the cytoplasm with consequences ranging from the activation of the cGAS/STING pathway, an innate immune response, to the creation of chromosomal instability. The discovery of those mechanisms has revolutionized the understanding of some inflammation-related diseases and the origin of complex chromosomal rearrangements, as observed during the initiation of tumorigenesis. Herein, we will highlight the complexity of the NE biology and discuss the clinical symptoms observed in NE-related diseases. The interplay between innate immunity, genomic instability, and nuclear envelope leakage could be a major focus in future years to explain a wide range of diseases and could lead to new classes of therapeutics.

Sign in / Sign up

Export Citation Format

Share Document