scholarly journals Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

2010 ◽  
Vol 11 (Suppl 1) ◽  
pp. S42 ◽  
Author(s):  
Mukul S Bansal ◽  
J Gordon Burleigh ◽  
Oliver Eulenstein
Keyword(s):  
Phylogenetic Analysis ◽  
Cost Models ◽  
Deep Coalescence ◽  
Genome Scale

An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships

2012 ◽  
Vol 25 (1) ◽  
pp. 1 ◽  
Author(s):  
Anna E. Syme ◽  
Daniel J. Murphy ◽  
Gareth D. Holmes ◽  
Stuart Gardner ◽  
Rachael Fowler ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Strong Support ◽  
Molecular Data ◽  
Species Level ◽  
Internal Transcribed Spacer Region ◽  
Deep Coalescence ◽  
History Of ◽  
Levels Of Support

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.

scholarly journals Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda

2021 ◽  
Author(s):  
Qing Zuo ◽  
Zhisheng Zhang ◽  
Yanjun Shen
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Divergence Time ◽  
Gene Arrangement ◽  
Phylogenetic Study ◽  
Relationship Of ◽  
Genome Scale ◽  
The Relationship

The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda and Pauropoda), but very little work has been done to explore their phylogenetic relationships. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: “TD (N\R) L + C” based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within Myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.

scholarly journals Whole-genome-based phylogeny of African swine fever virus

2020 ◽  
Vol 13 (10) ◽  
pp. 2118-2125
Author(s):  
Levon Aslanyan ◽  
Hranush Avagyan ◽  
Zaven Karalyan
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
A Genome ◽  
Genotype 2 ◽  
Genome Scale

Aim: A genome-scale phylogenetic analysis was used to infer the evolutionary dynamics of Asfarviridae – African swine fever virus (ASFV) – and better define its genetic diversity. Materials and Methods: All complete ASFV genomes from NCBI's resource as of March 2020 were used. The phylogenetic analysis used maximum likelihood and neighbor-joining methods. The evolutionary models detection was done with the help of the package of programs MEGA-X. Algorithms were used to build phylogenetic trees for type B DNA polymerases of ASFV (n=34) and HcDNAV (n=2), as an external group. Results: An expedient categorization of the Asfarviridae family uses five clades. Genotype 1 (except for LIV 5/40 virus isolate) as well genotype 7 are assigned to the alpha clade; genotype 2 to the beta clade; genotypes 8, 9, and 10 to the gamma clade; genotype 5 to the delta clade; and genotypes 3, 4, and 20, as well as genotype 22 and the LIV 5/40 isolate to the epsilon clade. Branch lengths on the phylogenetic tree are proportional to genetic distance along the branch. Branches at the phylogenetic tree of Asfarviridae are much shorter than branches for Baculoviridae. Shorter branches in ASFVs population suggest that Asfarviridae evolved relatively recently and remain more closely related. Conclusion: We suggest applying more robust standards using whole genomes to ensure the correct classification of ASFV and maintain phylogeny as a useful tool.

Characterisation of the novel clinical isolate X-4 containing a new tp0548 sequence-type

2020 ◽  
pp. sextrans-2020-054687
Author(s):  
Dan Liu ◽  
Man-Li Tong ◽  
Li-Li Liu ◽  
Li-Rong Lin ◽  
Hui-Lin Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Clinical Isolate ◽  
Phase Variation ◽  
Sequence Type ◽  
The Novel ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Sequencing Method ◽  
Genome Scale

ObjectivesA novel tp0548 sequence-type was identified in one clinical isolate (X-4) from a patient diagnosed with primary syphilis in Xiamen, China. To precisely define and characterise a new clinical isolate, we performed further genome-scale molecular analysis.MethodsThe pooled segment genome sequencing method followed by Illumina sequencing was performed.ResultsThis novel sequence-type contained a unique nucleotide substitution ‘T’ at position 167 and belonged to the SS14-like clade of TPA strains, as determined by phylogenetic analysis. Multi-locus sequence analysis of nine chromosomal loci demonstrated that the X-4 isolate was clustered within a monophyletic group of TPA strains. Whole-genome phylogenetic analysis subsequently corroborated the TPA strain classification of the X-4 isolate and revealed that the isolate was closely related to the SS14 strain, with 42 single-nucleotide variations and 12 insertions/deletions. In addition, high intrastrain heterogeneity in the length of the poly G/C tracts was found in the TPAChi_0347 locus, which might indicate that this gene of the X-4 isolate is likely involved in phase variation events. The length heterogeneity of the poly A/T tracts was lower than the genetic variability of the poly G/C tracts, and all the observed intrastrain variations fell within coding regions.ConclusionThe novel tp0548 sequence-type was determined to belong to a new TPA isolate, X-4. The identification of variable length in homopolymetic tracts (G/C and A/T) could provide a snapshot of the genes that potentially involved in genotype–phenotype variations. These findings provide an unequivocal characterisation for better understanding the molecular variation of this emerging isolate.

The Development of Not-For-Profit Hospital Cost Models

1988 ◽  
Vol 6 (1) ◽  
pp. 35-48
Author(s):  
Greg M. Thibadoux ◽  
Nicholas Apostolou ◽  
Ira S. Greenberg
Keyword(s):  
Hospital Cost ◽  
Cost Models ◽  
For Profit ◽  
Not For Profit

Morphological, histological and molecular characterization of Myxidium cf. rhodei infecting the kidney of Rutilus rutilus

2020 ◽  
Vol 141 ◽  
pp. 39-46
Author(s):  
MD Dorjievna Batueva ◽  
X Pan ◽  
J Zhang ◽  
X Liu ◽  
W Wei ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rutilus Rutilus ◽  
Longitudinal Axis ◽  
Suture Line ◽  
Present Species ◽  
Supplementary Data

In the present study, we provide supplementary data for Myxidium cf. rhodei Léger, 1905 based on morphological, histological and molecular characterization. M. cf. rhodei was observed in the kidneys of 918 out of 942 (97%) roach Rutilus rutilus (Linnaeus, 1758). Myxospores of M. cf. rhodei were fusiform with pointed ends, measuring 12.7 ± 0.1 SD (11.8-13.4) µm in length and 4.6 ± 0.1 (3.8-5.4) µm in width. Two similar pear-shaped polar capsules were positioned at either ends of the longitudinal axis of the myxospore: each of these capsules measured 4.0 ± 0.1 (3.1-4.7) µm in length and 2.8 ± 0.1 (2.0-4.0) µm in width. Polar filaments were coiled into 4 to 5 turns. Approximately 18-20 longitudinal straight ridges were observed on the myxospore surface. The suture line was straight and distinctive, running near the middle of the valves. Histologically, the plasmodia of the present species were found in the Bowman’s capsules, and rarely in the interstitium of the host. Phylogenetic analysis revealed that M. cf. rhodei was sister to M. anatidum in the Myxidium clade including most Myxidium species from freshwater hosts.

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