scholarly journals Genetic Variation Among Certain Fish Species in Terms of Evolution and Lineages

2021 ◽  
Vol 34 (2) ◽  
pp. 147-160
Author(s):  
Hussein A. Saud ◽  
Ilham J. J. Alshami
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Similarity ◽  
Rna Folding ◽  
Orthologous Gene ◽  
Minimum Free Energy ◽  
Minimum Evolution ◽  
Genetic Affinity ◽  
Maximum Likelihood Tree ◽  
Sox3 Gene ◽  
Common Ancestors

Three tests of phylogenetic including likelihood-joining tree, neighbour-joining tree, and minimum evolution tree have been used based on sox3 gene. Phylogenetic analysis was used to detect the genetic affinity and common ancestors for selected species that belong to the same or different families. This study showed the most appropriate methods for testing the genetic affinity among species and the methodology of each test according to the requirement of molecular applications. Secondary RNA predicted structure and minimum free energy were also included in this study because of their contribution to the detection of the orthologous gene and variance in RNA folding among species related to the different families. The genetic distance in the studied populations was calculated to know the most appropriate way to find out the genetic similarity among the studied species. The low distance-variance value of each group indicated significant genetic affinity among the species of the same family, this result is more consistent with the test of maximum-likelihood tree indicating the validity of this test to measure the genetic affinity among species that have common ancestors.

scholarly journals Molecular Characterization and Phylogenetic Analysis of MADS-Box Gene VroAGL11 Associated with Stenospermocarpic Seedlessness in Muscadine Grapes

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 232
Author(s):  
M Atikur Rahman ◽  
Subramani P Balasubramani ◽  
Sheikh M Basha
Keyword(s):  
Phylogenetic Analysis ◽  
Phosphorylation Site ◽  
Orthologous Gene ◽  
Mads Box ◽  
Vitis Species ◽  
Vitis Rotundifolia ◽  
Seed Content ◽  
Putative Phosphorylation Site ◽  
Mads Box Gene ◽  
Muscadine Grapes

Reduced expression of MADS-box gene AGAMOUS-LIKE11 (VviAGL11) is responsible for stenospermocarpic seedlessness in bunch grapes. This study is aimed to characterize the VviAGL11 orthologous gene (VroAGL11) in native muscadine grapes (Vitis rotundifolia) at the molecular level and analyze its divergence from other plants. The VroAGL11 transcripts were found in all muscadine cultivars tested and highly expressed in berries while barely detectable in leaves. RT-PCR and sequencing of predicted ORFs from diverse grape species showed that AGL11 transcripts were conservatively spliced. The encoded VroAGL11 protein contains highly conserved MADS-MEF2-like domain, MADS domain, K box, putative phosphorylation site and two sumoylation motifs. The muscadine VroAGL11 proteins are almost identical (99%) to that of seeded bunch cultivar, Chardonnay, except in one amino acid (A79G), but differs from mutant protein of seedless bunch grape, Sultanina, in two amino acids, R197L and T210A. Phylogenetic analysis showed that AGL11 gene of muscadine and other Vitis species formed a separate clade than that of other eudicots and monocots. Muscadine grape cultivar “Jane Bell” containing the highest percentage of seed content in berry (7.2% of berry weight) had the highest VroAGL11 expression, but almost none to nominal expression in seedless cultivars Fry Seedless (muscadine) and Reliance Seedless (bunch). These findings suggest that VroAGL11 gene controls the seed morphogenesis in muscadine grapes like in bunch grape and can be manipulated to induce stenospermocarpic seedlessness using gene editing technology.

scholarly journals Phylogenetic analysis of Na+/H+ (NuoL/MrpA) antiporters

2019 ◽  
pp. 8-15
Author(s):  
Lenin Sánchez-Calderón ◽  
Mauricio Nahuam Chávez-Avilés ◽  
Alma Laura Díaz-Pérez ◽  
Blanca Estela Gómez-Luna ◽  
Juan Carlos Ramírez-Granados ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Atp Synthesis ◽  
Domain Analysis ◽  
Phylogeny Reconstruction ◽  
Monovalent Cations ◽  
Minimum Evolution ◽  
Homologous Proteins ◽  
Conserved Domain ◽  
Low Concentrations ◽  
Eukaryotic Proteins

Objectives: Sodium/proton (Na+/H+) antiporters NuoL/MrpA-like proteins are important in monovalent cations homeostasis, ATP synthesis, are involved in growth using low concentrations of acetate, and in management of protons during methane production. To learn more about the evolutive origin and biological relevance of this protein, in this work a phylogenetic analysis of the NuoL/MrpA superfamily of proteins was done. Methodology: Phylogeny reconstruction was done with 596 NuoL/MrpA proteins and 39 MrpD-NuoM/N proteins. The algorithms used were minimum evolution and maximum likelihood, using MEGA program. Additionally, a conserved domain analysis was done. Contribution: NuoL/MrpA superfamily and their homologous proteins, MrpD-NuoM/N, form two paralogous groups. The NuoL/MrpA superfamily consists of two families. Family NuoL consist of arqueal, bacterial and eukaryotic proteins of around 600 aa in size. Family MrpA are formed by proteins from bacteria and archaea, with a 600 to 850 aa in size. Using the phylogenetic analysis and conserved domain analysis, a superfamily NuoL/MrpA evolution model was proposed.

Phylogenetic analysis of DNA sequence data.

2021 ◽  
pp. 265-282
Author(s):  
Sergei A. Subbotin
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Phylogenetic Study ◽  
Public Database ◽  
Sample Collection ◽  
Minimum Evolution ◽  
Molecular Phylogenetic ◽  
Pcr Products ◽  
Selection Of

Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.

scholarly journals PRACTICALITY AND TIME COMPLEXITY OF A SPARSIFIED RNA FOLDING ALGORITHM

2012 ◽  
Vol 10 (02) ◽  
pp. 1241007 ◽  
Author(s):  
SLAVICA DIMITRIEVA ◽  
PHILIPP BUCHER
Keyword(s):  
Time Complexity ◽  
Rna Folding ◽  
Minimum Free Energy ◽  
Energy Structure ◽  
Base Pairing ◽  
Time Analysis ◽  
Folding Algorithm ◽  
Run Time Analysis ◽  
Run Time ◽  
Standard Energy

Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n3). Recently, it has been claimed that RNA folding can be achieved in average time O(n2) using a sparsification technique. A proof of quadratic time complexity was based on the assumption that computational RNA folding obeys the "polymer-zeta property". Several variants of sparse RNA folding algorithms were later developed. Here, we present our own version, which is readily applicable to existing RNA folding programs, as it is extremely simple and does not require any new data structure. We applied it to the widely used Vienna RNAfold program, to create sibRNAfold, the first public sparsified version of a standard RNA folding program. To gain a better understanding of the time complexity of sparsified RNA folding in general, we carried out a thorough run time analysis with synthetic random sequences, both in the context of energy minimization and base pairing maximization. Contrary to previous claims, the asymptotic time complexity of a sparsified RNA folding algorithm using standard energy parameters remains O(n3) under a wide variety of conditions. Consistent with our run-time analysis, we found that RNA folding does not obey the "polymer-zeta property" as claimed previously. Yet, a basic version of a sparsified RNA folding algorithm provides 15- to 50-fold speed gain. Surprisingly, the same sparsification technique has a different effect when applied to base pairing optimization. There, its asymptotic running time complexity appears to be either quadratic or cubic depending on the base composition. The code used in this work is available at: http://sibRNAfold.sourceforge.net/ .

scholarly journals Identification and distribution of whiteflies (Hemiptera: Aleyrodidae) in tomato crops (Solanum lycopersicum) in Cundinamarca (Colombia)

2016 ◽  
Vol 34 (1) ◽  
pp. 42-50 ◽  
Author(s):  
Jorge E. Ángel D. ◽  
Julián Martínez H. ◽  
Mikol Santamaria G. ◽  
Sandra Parada P. ◽  
Everth Ebratt R.
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Similarity ◽  
Trialeurodes Vaporariorum ◽  
Wide Distribution ◽  
Specific Primers ◽  
Tomato Crop ◽  
Rio Negro ◽  
Structured Groups ◽  
Biotype B

The main purpose of this study was to determine the presence, distribution and characterization of whiteflies in thirteen tomato-crop producing municipalities in Cundinamarca (Colombia). Immature stages were collected and taken to the laboratory until adults emerged in order to establish their taxonomic identification. The mitochondrial regions were amplified with specific primers, which allowed for the allocation of biotypes in Bemisia tabaci. Genetic similarity analysis was performed in Trialeurodes vaporariorum using RAPD and phylogenetic analysis of the gene sequences mtCOI. The presence of T. vapo- rariorum was established in 100% of the municipalities visited and B. tabaci biotype B was detected in 32%, coexisting with T. vaporariorum. A wide distribution of T. vaporariorum was determined between 653 and 2,680 m a.s.l. B. tabaci was found between 653 and 1,940 m a.s.l distributed in four municipalities in the Sumapaz, lower Magdalena, and Rio Negro provinces. The RAPD analysis established high genetic similarity between the T. vaporariorum insects. The phylogenetic analysis did not allow for the resolution of structured groups inside the analyzed T. vaporariorum samples.

scholarly journals Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species

2019 ◽  
Author(s):  
Eun-Young Hwang ◽  
He Wei ◽  
Steven G. Schroeder ◽  
Edward W. Fickus ◽  
Charles V. Quigley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Nucleotide Diversity ◽  
Population Expansion ◽  
Orthologous Gene ◽  
Evolutionary Selection ◽  
Gene Sets ◽  
Sister Clade ◽  
The Face

ABSTRACTWe estimated average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity and the other perennials except G. tomentella had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except G. cyrtoloba and G. stenophita formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships, G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Neutrality selection tests within species showed that most genes were subjected to a recent directional selection due to a selective sweep or rapid population expansion. Although most gene sequence had negative and significant Tajima’s D, the sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced very similar evolutionary selection as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggested the perennials as potential sources of heat and drought resistance that will be of value in the face of climate change.

scholarly journals Molecular Taxonomy and Phylogenetic Analysis of Dove and Pigeon Species (Aves: Columbidae) of Pakistan, Based on COI Region of Mitochondrial DNA

2020 ◽  
Vol 7 (3) ◽  
pp. 35-44
Author(s):  
Fakhar -i-Abbas ◽  
Fakhar -i-Abbas ◽  
Fakhra Nazir ◽  
Fida Muhammad Khan
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Taxonomy ◽  
Columba Livia ◽  
Taxonomic Diversity ◽  
Coi Gene ◽  
Maximum Parsimony Tree ◽  
Maximum Likelihood Tree ◽  
Wide Range ◽  
Parsimony Tree

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, Maximum parsimony tree and UPGMA tree. In the current study, COI gene barcoding and phylogenetic analysis of family Columbidae gave results of multiple alignment which showed that Columba livia livia and Columba eversmanni, closely resembled as well as Spilopelia senegalensis and Streptopelia decaocta. While Streptopelia tranquebarica and Spilopelia chinensis have great affinity due to small clade difference and Treron phoenicoptera was distinctly related to other species due to large clade difference.

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