RECONSTRUCTION OF EVOLUTION OF GENOME STRUCTURES WITH PARALOGS

2021 ◽  
Vol 1 (19) ◽  
pp. 207-209
Author(s):  
K.Yu. Gorbunov
Keyword(s):  
Phylogenetic Tree ◽  
Multiplicative Error

For any weighted directed chain-cycle graphs a and b (referred to as structures) and any equal costs of operations (intermergings and duplication), we obtain an algorithm which, by successively applying these operations to a, outputs b if the first structure contains no paralogs (edges with a repeated name) and the second has no more than two paralogs for each edge. The algorithm has a multiplicative error of at most 13/9 + ε, where ε is any strictly positive number, and its runtime is of the order of no(ε–2.6), where n is the size of the initial pair of graphs. We also obtain algorithms for reconstruction of the evolution of genome structures with a condition on ancestor structures and along the phylogenetic tree.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

THREE-DIMENSIONAL VISUALIZATION FOR PHYLOGENETIC TREE

2017 ◽  
Vol 9 (4) ◽  
pp. 59-66
Author(s):  
M. Forghani ◽  
P. Vasev ◽  
V. Averbukh
Keyword(s):  
Phylogenetic Tree ◽  
Three Dimensional

Method of constructing phylogenetic tree based on fuzzy clustering

2009 ◽  
Vol 29 (3) ◽  
pp. 836-838
Author(s):  
Gang-cheng LI ◽  
Zan-bo LIU ◽  
Qing-guang ZENG
Keyword(s):  
Phylogenetic Tree ◽  
Fuzzy Clustering

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

Systematics and evolution of Lentibulariaceae: II. Genlisea

2018 ◽  
Author(s):  
Andreas Fleischmann
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
Karyotype Evolution ◽  
Distribution Map ◽  
Genome And Karyotype Evolution

Systematics and evolution of Genlisea (corkscrew plants) (Lentibulariaceae) are treated. Vegetative and generative morphology of the plants, and anatomy of their rhizophylls (‘root-leaves’) that function as sophisticated eel traps are explained and illustrated. A simplified phylogenetic tree and a detailed distribution map are provided, and the evolutionary history, including genome and karyotype evolution, and phylobiogeography of the 30 currently known species of Genlisea are discussed.

Systematics and evolution of Lentibulariaceae: I. Pinguicula

2018 ◽  
Author(s):  
Andreas Fleischmann ◽  
Aymeric Roccia
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary History ◽  
Infrageneric Classification ◽  
Distribution Maps

Systematics and evolution of Pinguicula (butterworts) (Lentibulariaceae) are treated. Vegetative and generative morphology of the genus are illustrated and interpreted in the light of available phylogenetic evidence. A new infrageneric classification is proposed for Pinguicula; a simplified phylogenetic tree and detailed distribution maps are provided. Evolutionary history and phylobiogeography are briefly discussed together with the habitats, ecology, and conservation of the genus.

DNA Barcoding and Phylogenetic Analysis Sugarcane (Saccharum officinarum L.) Based on matK ( maturase K) Gene

2020 ◽  
Vol 840 ◽  
pp. 162-170
Author(s):  
Ganies Riza Aristya ◽  
Fauzana Putri ◽  
Rina Sri Kasiamdari ◽  
Arni Musthofa
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Level ◽  
Economic Value ◽  
Saccharum Officinarum ◽  
Saccharum Spontaneum ◽  
Dna Barcodes ◽  
Pcr Method ◽  
Hybrid Cultivar ◽  
I Gene ◽  
Sequencing Process

Sugarcane (Saccharum officinarum L.) is an agricultural commodities with a great extent of diversity and high economic value. In Indonesia, the great extent of diversity of sugarcane is evidenced by a large number of cultivars cultivated. Sugarcane diversities at the molecular level can be seen using DNA barcodes, one of which is the matK. The purpose of the study was to identify and characterize matK and reconstruct the phylogenetic tree to determine the phylogeny of 24 sugarcane cultivars Indonesia. matK was amplified using the PCR method with matK F-5’ATGATTAATTAAGAGTAAGAGGAT-3’ and matK R-5’AATGCAAAAATTCGAAGGGT-3. Results showed that the matK gene was successfully amplified as many as 1531 bp. The sequencing process was done to determine the nucleotide sequence and compared with those of the GenBank database. It showed that the samples used had a similarity of 98.87%-99.44% to that of matK in Saccharum officinarum, Saccharum hybrid cultivar and Saccharum spontaneum. Reconstruction of the phylogenetic tree showed that the samples used were located in the same clade with a zero genetic distance, while all the references from NCBI were also located in the same clade. The analysis of genetic variation indicated that it had no haplotype value.

Recombination, Balancing Selection and Phylogenies in MHC and Self-Incompatibility Genes

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1833-1844 ◽  
Author(s):  
Mikkel H Schierup ◽  
Anders M Mikkelsen ◽  
Jotun Hein
Keyword(s):  
Major Histocompatibility Complex ◽  
Phylogenetic Tree ◽  
Balancing Selection ◽  
Nucleotide Sequences ◽  
Recombination Process ◽  
Self Incompatibility ◽  
Selection Coefficient ◽  
Histocompatibility Complex ◽  
A Site ◽  
Possible Cause

AbstractUsing a coalescent model of multiallelic balancing selection with recombination, the genealogical process as a function of recombinational distance from a site under selection is investigated. We find that the shape of the phylogenetic tree is independent of the distance to the site under selection. Only the timescale changes from the value predicted by Takahata's allelic genealogy at the site under selection, converging with increasing recombination to the timescale of the neutral coalescent. However, if nucleotide sequences are simulated over a recombining region containing a site under balancing selection, a phylogenetic tree constructed while ignoring such recombination is strongly affected. This is true even for small rates of recombination. Published studies of multiallelic balancing selection, i.e., the major histocompatibility complex (MHC) of vertebrates, gametophytic and sporophytic self-incompatibility of plants, and incompatibility of fungi, all observe allelic genealogies with unexpected shapes. We conclude that small absolute levels of recombination are compatible with these observed distortions of the shape of the allelic genealogy, suggesting a possible cause of these observations. Furthermore, we illustrate that the variance in the coalescent with recombination process makes it difficult to locate sites under selection and to estimate the selection coefficient from levels of variability.

scholarly journals Structure Unveils Relationships between RNA Virus Polymerases

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 313
Author(s):  
Heli A. M. Mönttinen ◽  
Janne J. Ravantti ◽  
Minna M. Poranen
Keyword(s):  
Phylogenetic Tree ◽  
Rna Viruses ◽  
Rna Virus ◽  
Sequence Similarity ◽  
Protein Structures ◽  
Structural Similarity ◽  
Functional Differentiation ◽  
Comparison Method ◽  
Homologous Structure ◽  
Biological Entities

RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.

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