scholarly journals Phylogenetic Study of African Combretaceae R. Br. based on rbcL Sequence

2019 ◽  
Vol 25 (2) ◽  
pp. 170-177
Author(s):  
Alfred Ossai Onefeli ◽  
Vidmantas Stanys
Keyword(s):  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Economic Value ◽  
Composite Index ◽  
Evolutionary Genetics ◽  
Phylogenetic Study ◽  
Medicinal Species ◽  
Multiple Sequence ◽  
Relationship Of

Combretaceae is an angiosperm family of high economic value. However, there is dearth of information on the phylogenetic relationship of the members of this family using ribulose biphosphate carboxylase (rcbL) gene. Previous studies with electrophoretic-based and morphological markers revealed that this family is phylogenetically complex. In the present study, 79 sequences of rbcL were used to study the phylogenetic relationship among the members of Combretaceae of African origin with a view to provide more information required for the utilization and management of this family. Multiple Sequence alignment was executed using the MUSCLE component of Molecular Evolutionary Genetics Version X Analysis (MEGA X). Transition/Transversion ratio, Consistency index, Retention Index and Composite Index were also determined. Phylogenetic trees were constructed using Maximum parsimony (MP) and Neighbor joining methods. The alignment of rcbL in the family Combretaceae shows 0.59 for both variation and parsimony sites with the overall mean distance of 0.71. Result shows that the genera Combretum, Terminalia are polyphyletic, while Conocarpus, Quisqualis and Meiostemon are monophyletic. Findings from this study can be applied to the scientific classification of the African Combretaceae, especially where morphological and electrophoretic-based molecular delimitation have failed. rbcL from this family can also be used as barcodes against drug adulteration of the medicinal species.

scholarly journals Genetic diversity and phylogenetic relationship of higher termite Globitermes sulphureus (Haviland)(Blattodea:Termitidae)

Sociobiology ◽  
2021 ◽  
Vol 68 (2) ◽  
pp. 5911
Author(s):  
Nurul Akmar Hussin ◽  
Abdul Hafiz Ab Majid
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Evolutionary Genetics ◽  
Neighbor Joining ◽  
Geographic Isolation ◽  
Neutral Genetic Diversity ◽  
Coii Gene ◽  
Relationship Of

The subterranean higher termite Globitermes sulphureus (Blattodea: Termitidae), is a peridomestic forager and regarded as a significant pest in Southeast Asia. In this study, the populations of G. sulphureus from the USM main campus area were investigated based on partial sequences of the mitochondrial COII gene. The genetic diversity was determined using DnaSP v5 software while the phylogenetic relationship was defined using Neighbor-joining (NJ) and maximum likelihood (ML) methods using Molecular Evolutionary Genetics Analysis (MEGA 7) software. A total of 2 haplotypes were detected among the 5 sample sequences that differed by two variable sites. In addition, both phylogenetic trees gave similar topology and supporting the results from haplotype diversity. Based on the haplotype diversity and molecular phylogeny, it is proposed that geographic isolation and lack of human activities have contributed to the neutral genetic diversity of G. sulphureus.   

Phylogenetic relationship of potato CAT1 and CAT2 genes, their differential expression in non-photosynthetic organs and during leaf development, and their association with different cellular processes

2006 ◽  
Vol 33 (7) ◽  
pp. 639 ◽  
Author(s):  
Isabel Santos ◽  
Helena Pires ◽  
José M. Almeida ◽  
Fernanda Fidalgo ◽  
Ana Confraria ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Activity Patterns ◽  
Developmental Phase ◽  
High Identity ◽  
Solanaceous Species ◽  
Cdna Sequences ◽  
Cellular Processes ◽  
Relationship Of ◽  
Expression And Activity

Plants contain multiple forms of catalase (CAT) and their specific functions remain uncertain. We cloned two potato cDNAs corresponding to CAT1 and CAT2 genes, analysed their phylogenetic relationship, and studied their expression and activity in different organs to gain clues to their functions. Phylogenetic trees and the alignment of CAT cDNA sequences provided evidence that CAT1 and CAT2 genes have high identity to catalases of other solanaceous species, but are not phylogenetically closely related to one another, which contradicts the phylogenetic closeness ascribed to these genes. Northern blot analyses revealed that expression of CAT genes is controlled by leaf developmental phase. CAT2 expression was higher in both very young and senescent leaves, whereas CAT1 mRNA accumulated mainly in mature leaf, where the lowest CAT2 expression occurred. CAT1 and CAT2 are also differentially expressed in root, sprout and petal. Expression and activity patterns are consistent with different physiological roles for CAT1 and CAT2 isoforms. CAT1 is considered to be associated with photorespiration whereas CAT2 would fulfill physiological roles unrelated to this process. CAT2 appears to be a multifunctional isoform, associated with glyoxysomal activity in leaf senescence, other processes in non-photosynthetic organs and defence, functions that in other solanaceous species are fulfilled by two different isoforms.

Description of new chiactine-bearing sponges provides insights into the higher classification of Calcaronea (Porifera: Calcarea)

Zootaxa ◽  
2019 ◽  
Vol 4615 (2) ◽  
pp. 201
Author(s):  
ADRIANA ALVIZU ◽  
JOANA R. XAVIER ◽  
HANS TORE RAPP
Keyword(s):  
New Species ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Phylogenetic Study ◽  
Two New Species ◽  
Close Relationship ◽  
New Material ◽  
Relationship Of ◽  
The Antarctic

A recent phylogenetic study revealed a close relationship between chiactine-bearing (family Achramorphidae, order Leucosolenida) and pugiole-bearing (order Baerida) calcaronean sponges as well as new putative taxa within Achramorphidae. In this study, we present a revision of chiactine-bearing sponges based on morphological re-examination of type material and recently collected specimens, in addition to new molecular data for the ribosomal 18S and C-region of the 28S. We provide re-descriptions for all known chiactine-bearing species, and further describe two new species from the Antarctic (Achramorpha antarctica sp. nov. and Megapogon schiaparellii sp. nov.) and two new species and a new genus from the Nordic Seas (Achramorpha ingolfi sp. nov. and Sarsinella karasikensis gen. nov. sp. nov.). The new phylogenetic reconstruction based on ribosomal 18S and C-region of the 28S confirms previous findings about the close relationship of some members of Baerida and the family Achramorphidae of the order Leucosolenida. However, new material and the addition of molecular data from the type species of both taxa would be required to formally propose changes at (sub-)ordinal levels within the classification of Calcaronean sponges. 

scholarly journals Phylogenetic relationship of Salmonella enterica strains in Tehran, Iran, using 16S rRNA and gyrB gene sequences

2011 ◽  
Vol 5 (06) ◽  
pp. 465-472 ◽  
Author(s):  
Mercedeh Tajbakhsh ◽  
Babak Noory Nayer ◽  
Kamyar Motavaze ◽  
Pedram Kharaziha ◽  
Mohsen Chiani ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Phylogenetic Relationship ◽  
Salmonella Enterica ◽  
Phylogenetic Trees ◽  
Gyrb Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Comparison Results ◽  
Relationship Of

Introduction: We assessed whether 16S rDNA and gyrB gene sequences, alone or combined, were suitable for determining the phylogenetic relationship among Salmonella enterica strains isolated from Tehran, Iran.  Patients over five years of age enrolled in an acute diarrheal surveillance project in Tehran province between May 2004 and October 2006 were selected as our study group.  Methodology: 16S ribosomal DNA (rDNA) and gyrB genes from 40 Salmonella isolates obtained from patients with acute diarrhea were sequenced and the data was used to generate phylogenetic trees that facilitated isolate comparison. Results: Salmonella strains clustered into five to seven phylogenetic groups, dependent on analysis of 16S rDNA (1546 bp), gyrB (1256 bp) or a combination of the two genes.  By 16S rDNA sequence analysis, only strains of Salmonella enterica  serovar Typhi ( S. Typhi)  clustered exclusively together.  gyrB sequences permitted clustering of all the S. Typhi and S. Paratyphi A isolates, and clustering of S. Enteritidis into two separate but exclusive groups.  Concatenation of the two data sets did not significantly improve the resolution of the strains compared to the gyrB gene.  None of the analyses completely resolved S. enterica Paratyphi B and C into mutually exclusive groups.   Conclusion: Sequencing of gyrB represents a potentially useful tool for determining the phylogenetic relationship of S. enterica strains in Tehran, Iran. Genetic analysis of the 16S rRNA gene alone or in combination with gyrB did not increase the resolution between serotypes of S. enterica.  We speculate that inclusion of additional genetic markers would improve the sensitivity of the analysis.

Phylogenetic relationship of Parmelia lindmanii (Parmeliaceae) inferred by analysis of its nuITS rDNA sequence

2010 ◽  
Vol 42 (4) ◽  
pp. 423-428 ◽  
Author(s):  
Sionara ELIASARO ◽  
Leonardo M. CRUZ ◽  
Marcello IACOMINI ◽  
Fabio de OLIVEIRA PEDROSA ◽  
Lucimara M. C. CORDEIRO
Keyword(s):  
Phylogenetic Relationship ◽  
Ribosomal Dna ◽  
Bayesian Approach ◽  
Type Species ◽  
Rdna Sequence ◽  
Phylogenetic Study ◽  
Nuclear Its ◽  
Relationship Of ◽  
The Relationship

AbstractUsing the nuclear ITS (nuITS) region of the ribosomal DNA and an MP/Bayesian approach, a phylogenetic study was carried out to evaluate the relationship of Parmelia lindmanii with other members of the parmelioid lichen group. Our results showed that P. lindmanii does not belong to the genus Myelochroa, as previously proposed, but is within the clade containing the type species of Parmelinella.

scholarly journals Molecular Phylogeny of Polyporales from Bafut Forest, Cameroon and Their Importance to Rural Communities

2019 ◽  
Vol 10 (2) ◽  
pp. 1
Author(s):  
Tonjock Rosemary Kinge ◽  
Azinue Clementine Lem ◽  
Seino Richard Akwanjoh
Keyword(s):  
Phylogenetic Analysis ◽  
Rural Communities ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationship ◽  
Local Communities ◽  
Medicinal Species ◽  
Forest Reserves ◽  
Phylogenetic Studies ◽  
Ctab Method ◽  
Relationship Of

The polyporales are a large order of pore fungi within the Basidiomycota (Kingdom Fungi). They are mostly found on decay wood with some edible and medicinal species and others causing diseases of trees. In Cameroon, the knowledge on the phylogeny of polyporales is limited, their historical uses as food, medicine, source of income and the sociological impacts are apparently threatened due to slow ethnomycology research drive. The aim of this study was to identify and determine the phylogenetic relationship of polyporales in the Bafut forest and document its uses to the local communities. DNA was extracted using CTAB method and amplified using primers ITS 1 and ITS4. Their identities were determined in GeneBank using BLAST and a phylogenetic analysis was done using MEGA version 7. For ethnomycological studies, a total of 180 semi structured questionnaires were used to collect information on traditional knowledge in four communities around the Bafut forest. Results from phylogenetic studies showed that, ten species were identified and belonged to seven genera comprising of the Microporus, Hexagonia, Ganoderma, Trametes, Favolus, Steccherinum and Cymatoderma which formed 7 independent monophyletic groups. Ethnomycological findings revealed that, polypores are used as food and medicine within these communities. Microporus xanthopus and Microporus vernicipes were used as food and medicine while all Trametes species were reported to be only medicinal. The Bafut people commonly called mushrooms “Boh” and those that grow on wood “Boh ti”. They usually differentiate the edible and nonedible mushroom using the term “yi kworu” and “yi tekworu”. Thus “Boh yi kworu” and “Boh yi tekworu” respectively. This study represents the first on the identification, phylogeny and uses of polyporales to the communities around the Bafut forest reserves and helps in their conservation.

scholarly journals The approach to the comparative morphological analysis of spores of the Pteridaceae E. D. M. Kirchn family representatives (Pteridophyta) based on phylogenetic relationship data

2020 ◽  
Vol 19 (2) ◽  
pp. 061-065
Author(s):  
A. V. Vaganov ◽  
M. V. Skaptsov ◽  
D. I. Kogtev
Keyword(s):  
Phylogenetic Relationship ◽  
Evolutionary Biology ◽  
Morphological Analysis ◽  
Natural Classification ◽  
Comparative Morphological Analysis ◽  
The Family ◽  
New Knowledge ◽  
Relationship Of

The work presents the result of using comparative morphological analysis of spore of threesubfamilies from the family Pteridaceae E. D. M. Kirchn. (Cryptogrammoideae S. Linds., Pteridoideae C. Chr.ex Crabbe, Jermy a. Mickel, Ceratopteridoideae (J. Sm.) R. M. Tryon) by evolutionary biology method by Mesquitesoftware. This approach allows comparing in detail the standardized qualitative features of the morphology of sporeswith the data on phylogenetic relationship of representatives, which as a result helps to identify intra- and intertaxonomicgroups of relationship, to search for evolutionary connections, to obtain new knowledge for solving problems in ferntaxonomy. Obtained data allow supplement natural classification of the Pteridaceae family.

scholarly journals Mutation and Phylogenetic Analysis of Spike Glycoprotein of Indonesian Isolates of Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2)

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Shabarni Gaffar ◽  
◽  
Syifa Al Fauziah Rahmani ◽  
Ari Hardianto
Keyword(s):  
Amino Acid ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Surface Protein ◽  
Amino Acid Sequences ◽  
Effective Vaccine ◽  
Neighbor Joining ◽  
Multiple Sequence ◽  
Spike Gene ◽  
Relationship Of

Coronavirus disease-2019 (COVID-19) is an infectious acute respiratory disease caused by SARS-CoV-2. The protein that plays a role in the entry of SARS-CoV-2 into human cells is the surface protein, or the Spike, which is thought to be the effective vaccine target to prevent SARS-CoV-2 infection. Until December 2020, Indonesia has reported 106 SARS-CoV-2 genome sequences identified from COVID-19 positive patients. The purpose of this study was to analyze the phylogenetic relationship of the Spike protein of the Indonesian isolates of SARS-CoV-2 Indonesian, as well as the virus mutations and their effects on changes in the amino acid. The 106 Indonesian SARS-CoV-2 genomes were downloaded from GISAID and the Spike nucleotide and amino acid sequences were analyzed by multiple sequence alignment (MSA) and mutation analysis using the ClustalW method. Phylogenetic trees were created using the Neighbor-Joining method in MEGA-X software. The results showed that 30 of the 106 Indonesian isolate SARS-CoV-2 Spike were 100% identical to the Wuhan-Hu-1, while the remaining 76 had experienced mutations at 1-4 sites. There were 43-point mutations in the Spike gene, 27 of which led to amino acid changes and four had not been reported in other countries. The global mutation D614G was found in 60 Indonesian isolates , of which West Java was the province with the most reports. The phylogenetic of Spike showed that the Indonesian samples have been divided into several branches that are far from Wuhan-Hu-1. This study indicates the possibility of differences in the protein structure of Indonesian isolate SARS-CoV-2 Spike that need to be further studied to manufacture a vaccine against the Indonesian strain of SARS-CoV-2.

scholarly journals Phylogenetic Relationship Within Genus Araucaria (Araucariaceae) Assessed by Means of AFLP Fingerprints

2006 ◽  
Vol 55 (1-6) ◽  
pp. 45-52 ◽  
Author(s):  
V. M. Stefenon ◽  
O. Gailing ◽  
R. Finkeldey
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Aflp Markers ◽  
Phylogenetic Study ◽  
The Family ◽  
Chloroplast Dna Sequences

Abstract Highly polymorphic AFLP markers were applied to analyse the phylogenetic relationships of seven species from three sections within genus Araucaria (Araucariaceae) with cladistic and phenetic approaches. The objectives of the study were to compare the intrageneric relationships within Araucaria assessed by AFLP markers with the classification according to chloroplast DNA sequences and morphological characters. The AMOVA revealed 48% of the variation among species. The results of the principal coordinate analysis revealed three distinct groups: (1) A. angustifolia and A. araucana (= section Araucaria), (2) A. bidwillii (= section Bunya) and (3) A. cunninghamii, A. heterophylla, A. rulei and A. scopulorum (= section Eutacta). In the cladistic and phenetic analyses, phylogenetic trees were subdivided into two sister clades, one comprising the samples from section Eutacta, the other one was divided again into two sister clades corresponding to sections Araucaria and Bunya. These results are congruent with a previous phylogenetic study of the family Araucariaceae based on rbcL sequences and with the classification of genus Araucaria based on morphological characters. Both rbcL sequence data and AFLP analyses do not support section Bunya as one of the oldest sections within genus Araucaria, as suggested by the fossil record. The utility of AFLP markers for phylogenetic analyses is discussed.

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