scholarly journals Phylogenetic analysis of lysine, threonine and butanol strain-producers

1970 ◽  
Vol 21 ◽  
pp. 288-292
Author(s):  
O. O. Tigunova ◽  
G. S. Andriiash ◽  
N. Ye. Beiko ◽  
S. M. Shulha
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Phylogenetic Relationships ◽  
Clostridium Acetobutylicum ◽  
Genomic Dna ◽  
Agarose Gel ◽  
Brevibacterium Flavum ◽  
Mutant Strains

Aim. Identify and confirm the taxonomic position of the obtained mutant strains Brevibacterium sp. IMB B-7447, Brevibacterium flavum IMB B-7446 and Clostridium acetobutylicum IMB B-7407 (IFBG C6H). Methods. A fragment of genomic DNA from agarose gel using «Macherey-Nagel NucleoSpin Extract» was isolated according to the instructions of the producer and sequenced. Comparative analysis using the program «BLAST-online» was done. Phylogenetic dendrograms using methods Neighbour joining and Maximum likelihood were created. Results. Dendrograms of phylogenetic relationships of studied strains and related strains of databases «GenBank» were constructed. Conclusions. Found that homology of Brevibacterium sp. 90 and Brevibacterium sp. IMB B-7447 is 98 %, and stains B. flavum TH7 and B. flavum IMB B-7446 classified to species C. glutamicum. Strain C. acetobutylicum IMB B-7407 (IFBG C6H) been reclassified to C. pasteurianum IFBG C6H. Keywords: genes 16S rRNA, dendrogram, stains-produsers.

scholarly journals Molecular identification of stone loaches of Choman River system, Tigris Basin, based on the Cytochrome b gene with an overview of the Cobitoidea Superfamily

2017 ◽  
Author(s):  
Edris Ghaderi ◽  
Hamid Farahmand ◽  
Barzan Bahrami Kamangar ◽  
Mohammad A. Nematollahi
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Maximum Likelihood ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
River System ◽  
Distinct Species ◽  
Molecular Data ◽  
Genetic Distances ◽  
Molecular Phylogenetic

AbstractMolecular data and phylogenetic relationships of four Choman loaches species (Oxynoemacheilus chomanicus, O. zagrosensis, O. kurdistanicus and Turcinoemacheilus kosswigi) recently morphologically described from western Iran were evaluated with 64 species from the Cobitoidea superfamily based on their cytochrome b sequences to exhibit the placement of the Choman loaches species within the Cobitoidea superfamily. A comparative analysis of Kimura-2-parameter (K2P) distances was accomplished using sequence divergences of Cobitoidea to calculate intra and interspecific in superfamily, family and genus taxa. The average intraspecific K2P genetic distances of Choman loaches species was 0.005 whereas this value was 0.016 for the Cobitoidea superfamily. Molecular phylogenetic relationships were assessed using Maximum likelihood and Bayesian methods. Dendrograms obtained by these methods revealed all four Choman loaches species as distinct species among other reported Nemacheilidae Spp. These species were clustered with Oxynoemacheilus and Turcinoemacheilus genera within other species in the Nemacheilidae family. The phylogenetic analysis revealed that Cobitoidea superfamily consists of nine families ((Gyrinocheilidae + Botiidae) + ((Catostomidae + Vaillentellidae) + ((Nemacheilidae + Cobitidae) + ((Ellopostomidae + Gastromyzontidae) + Balitoridae)))) and indicated Nemacheilidae is a valid and distinct family from Balitoridae.

Whale falls, multiple colonisations of the deep, and the phylogeny of Hesionidae (Annelida)

2015 ◽  
Vol 29 (2) ◽  
pp. 105 ◽  
Author(s):  
Mindi Summers ◽  
Fredrik Pleijel ◽  
Greg W. Rouse
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Deep Sea ◽  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Shallow Waters ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
New Members

Phylogenetic relationships within Hesionidae Grube, 1850 are assessed via maximum parsimony and maximum likelihood analyses of mitochondrial (cytochrome c oxidase subunit I and 16S rRNA) and nuclear (18S rRNA, and 28S rRNA) data. The analyses are based on 42 hesionid species; six of these being new species that are described here. The new species, all from deep (>200 m depth) benthic environments (including whale falls) in the eastern Pacific, are Gyptis shannonae, sp. nov., Neogyptis julii, sp. nov., Sirsoe sirikos, sp. nov., Vrijenhoekia ketea, sp. nov., Vrijenhoekia falenothiras, sp. nov., and Vrijenhoekia ahabi, sp. nov. The molecular divergence among the new members of Vrijenhoekia is pronounced enough to consider them cryptic species, even though we cannot distinguish among them morphologically. Our results also showed that the subfamily Hesioninae Grube, 1850, as traditionally delineated, was paraphyletic. We thus restrict Hesioninae to include only Hesionini Grube, 1850 and refer the remaining members to Psamathinae Pleijel, 1998. The present study increases the number of hesionid species associated with whale falls from one to six and markedly increases the number of described deep-sea hesionid taxa. There appear to have been multiple colonisations of the deep sea from shallow waters by hesionids, though further sampling is warranted.

Detection of the Na+-translocating NADH-quinone reductase in marine bacteria using a PCR technique

2000 ◽  
Vol 46 (4) ◽  
pp. 325-332 ◽  
Author(s):  
Sanae Kato ◽  
Isao Yumoto
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
16S Rrna ◽  
Marine Bacteria ◽  
Genomic Dna ◽  
Screening Method ◽  
Quinone Reductase ◽  
Amino Acid Sequences ◽  
Homologous Sequences ◽  
Simple Screening

To examine the distribution of the Na+-translocating NADH-quinone reductase (Na+-NQR) among marine bacteria, we developed a simple screening method for the detection of this enzyme. By reference to the homologous sequences of the Na+-NQR operons from Vibrio alginolyticus and Haemophilus influenzae, a pair of primers was designed for amplification of a part of the sixth ORF (nqr6) of the Na+-NQR operon. When PCR was performed using genomic DNA from 13 marine bacteria, a 0.9-kbp fragment corresponding to nqr6 was amplified in 10 strains. Although there were three PCR-negative strains phylogenetically, based on the sequence of the 16S rRNA, these were placed far from the PCR-positive strains. No product was observed in the case of nonmarine bacteria. The nucleotide and predicted amino acid sequences of nqr6 were highly conserved among the PCR-positive marine bacteria. A phylogenetic analysis of marine bacteria, based on nqr6 sequencing, was performed.Key words: Na+-translocating, NADH-quinone reductase, marine bacteria, PCR.

Molecular phylogeny of the butterfly tribe Baorini Doherty, 1886 (Hesperiidae, Hesperiinae) in China

Zootaxa ◽  
2019 ◽  
Vol 4565 (1) ◽  
pp. 108 ◽  
Author(s):  
WEIBIN JIANG ◽  
HAIYAN HE ◽  
YUANYUAN LI ◽  
YING WANG ◽  
CHEN GE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Species Diversity ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Mitochondrial Genes ◽  
Nuclear Genes ◽  
Large Group ◽  
The Status

The butterfly tribe Baorini Doherty, 1886 is a large group of skippers. In this study, a total of 8 genera and 41 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2084 bp). Phylogenetic relationships and subdivision of this tribe were investigated and the status of the genera are discussed. Partitioned maximum likelihood analyses were performed based on the combined dataset. Our results suggest that the data are split into two well-supported clades in the phylogeny tree. This analysis also represents the most complete phylogenetic analysis of the tribe Baorini in China to date, and includes several genera and species that have been previously excluded from published phylogenies of this group. 

scholarly journals Identification and Characterization of Staphylococcus aureus 16S rRNA gene isolated from different Food Specimens from South Indian Region

2020 ◽  
Vol 10 (5) ◽  
pp. 24-32
Author(s):  
Mondeddu Kiran Kumar ◽  
Charu Tyagi ◽  
Arjun Sahu ◽  
Nalini Desai ◽  
Jayanand Manjhi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Infection Rate ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Food Borne

Staphylococcus aureus (S. aureus) associated food-borne diseases have global impact on human health. Genome wide analyses have shown that S. aureus contains specific endotoxin expressing gene and produce toxic proteins which is responsible for food contamination. Appropriate detection of pathogens is one of the major tool to avoid infection rate and reduce the health and socio-economic burden to human being. In addition, inappropriate handing the specimens, misdiagnosis and limited standard medical support could directly influence the infection rate. The objective of this study was to identify S. aureus from different food specimens from Hyderabad, India. A total of 70 random bacterial nutrient agar medium pure plates were made based on different morphological appearance of bacterial colonies. Preliminary identification of S. aureus based on standardized morphological method showed specific golden yellow colonies. Biochemical assay also verified bacterial specimens. Furthermore, molecular characterization was performed on the basis of polymerase chain reaction (PCR) and sequencing of 16S rRNA gene of S. aureus. Newly sequenced 16S rRNA gene sequences showed 100% homology to S. aureus, analyzed using NCBI-BLAST tool. The phylogenetic analysis and nucleotide base composition studies performed using 39 sequences of 16S rRNA gene from different isolates of Staphylococcus, including Staphylococcus aureus. For the purpose, 16S rRNA gene sequences were retrieved from the NCBI in FASTA format. The phylogenetic analysis was performed using Maximum Likelihood method and revealed the relationships and percent similarity of Staphylococcus aureus 16S rRNA gene. Keywords: Food-borne diseases; 16S rRNA gene; Maximum Likelihood; Phylogenetic analysis; Staphylococcus aureus.

scholarly journals Pontibacter xinjiangensis sp. nov., in the phylum ‘Bacteroidetes’, and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov.

2010 ◽  
Vol 60 (1) ◽  
pp. 99-103 ◽  
Author(s):  
Yang Wang ◽  
Kundi Zhang ◽  
Feng Cai ◽  
Lei Zhang ◽  
Yali Tang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
Taxonomic Approach ◽  
Sequence Similarities

A novel strain, designated 311-10T, isolated from soil of Xinjiang, China, was characterized by using a polyphasic taxonomic approach. The isolate was Gram-negative, aerobic, rod-shaped, non-motile, oxidase-negative and catalase-positive. The predominant menaquinone of strain 311-10T was MK-7 and the genomic DNA G+C content was 47.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate formed a cluster with the genera Pontibacter and [Effluviibacter] in the phylum ‘Bacteroidetes’, with sequence similarities of 93.9–95.6 %. Phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses support the reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov. (type strain, SRC-1T=MTCC 7260T=DSM 17521T) and the establishment of a novel species, Pontibacter xinjiangensis sp. nov., with strain 311-10T (=CCTCC AB 207200T=NRRL B-51335T) as the type strain.

scholarly journals Phylogenetic Analysis of Mandarin Landraces, Wild Mandarins, and Related Species in China Using Nuclear LEAFY Second Intron and Plastid trnL-trnF Sequence

2007 ◽  
Vol 132 (6) ◽  
pp. 796-806 ◽  
Author(s):  
Li Yingzhi ◽  
Cheng Yunjiang ◽  
Tao Nengguo ◽  
Deng Xiuxin
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Average Length ◽  
Hybrid Origin ◽  
Data Sets ◽  
Citrus Reticulata ◽  
F Region ◽  
Plausible Hypothesis

Nucleotide sequences of the second intron of the nuclear LEAFY gene (FLint2) and trnL-trnF region of the chloroplast genome were used to analyze the phylogenetic relationships among eight wild mandarins (Citrus reticulata Blanco), 19 mandarin landraces, and 19 related species of Citrus L. Forty-six trnL-trnF sequences and 111 FLint2 sequences were obtained from 46 ingroup accessions, with an average length of 1059.7 and 776.7 bp respectively. Phylogeny reconstructions were conducted separately for these two data sets using maximum parsimony and maximum likelihood criteria. Monophyly of mandarins was supported by both of these data sets, and in this clade, most mandarin landraces formed an unresolved polytomy, whereas ‘Jiangyong 1’, ‘Chongyi A2’, ‘Chongyi A1’ (or ‘Jiangyong 4’ in FLint2 data), and ‘Daoxian 1’ wild mandarins formed a subclade. ‘Mangshan A1’ and ‘Daoxian 5’ wild mandarins were sisters to this mandarin clade. A hybrid origin of five mandarin landraces and several mandarin-related species was suggested as a plausible hypothesis to explain the incongruence between the FLint2 and trnL-trnF data sets.

scholarly journals Interspecific Relationships in Pistacia Based on RAPD Fingerprinting

HortScience ◽  
2002 ◽  
Vol 37 (1) ◽  
pp. 168-171 ◽  
Author(s):  
Salih Kafkas ◽  
Rafael Perl-Treves
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Phylogenetic Relationships ◽  
Genomic Dna ◽  
Rapd Analysis ◽  
Leaf Tissue ◽  
Distinct Species ◽  
Randomly Amplified Polymorphic Dna ◽  
Specific Level ◽  
Rapd Fingerprinting

Phylogenetic relationships among nine species in the genus Pistacia were studied by randomly amplified polymorphic DNA (RAPD) analysis. The following species were included: P. atlantica, P. terebinthus, P. eurycarpa, P. vera, P. integerrima, P. mexicana, P. palaestina, P. lentiscus, and P. khinjuk. Genomic DNA was extracted from leaf tissue and RAPD analysis was performed using 20 primers. A total of 242 fragments were generated and 228 bands were polymorphic at the inter-specific level. Subjecting these data to phylogenetic analysis yielded a shortest cladogram that is 338 steps long, featuring two main groups. P. vera, P. khinjuk, P. eurycarpa, P. atlantica, and P. integerrima were included in one group, while P. terebinthus, P. palaestina, P. mexicana, and P. lentiscus formed the second group. The first group included species with single-trunked and big trees, whereas the species included in the second group mostly grow as shrubs or small trees. The cladogram showed that the closest pairs of species were P. terebinthus and P. palaestina, P. eurycarpa and P. atlantica, P. vera and P. khinjuk, and P. mexicana and P. lentiscus. We suggest that P. palaestina is in fact a variety of P. terebinthus in view of the small genetic distance between them. This study also showed that P. eurycarpa (syn. P. atlantica var. kurdica) is a distinct species from P. atlantica, rather than a variety within the same species.

Phylogenetic relationships of Echeveria (Crassulaceae) and related genera from Mexico, based on three DNA barcoding loci

Phytotaxa ◽  
2019 ◽  
Vol 422 (1) ◽  
pp. 33-57 ◽  
Author(s):  
LUIS E. DE LA CRUZ-LÓPEZ ◽  
FRANCISCO VERGARA-SILVA ◽  
JERÓNIMO REYES SANTIAGO ◽  
GABRIELA ESPINO ORTEGA ◽  
PABLO CARRILLO-REYES ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Dna Barcoding ◽  
Phylogenetic Relationships ◽  
Consensus Trees ◽  
As Species ◽  
Tree Inference ◽  
Selection Of

Mexico is considered as diversification and endemism center of the genus Echeveria. Previous tree inference studies have shown the genus to be non-monophyletic in relation to other genera, but sampling for Echeveria has been poor, and has not allowed to understand the relationships within the genus. In this work, Bayesian and maximum likelihood phylogenetic analysis were performed, using a combined standard DNA barcoding loci matrix (rbcL, matK and ITS2) and GenBank ITS2 accessions for Graptopetalum, some Sedum and few Echeveria taxa. The selection of taxa encompasses all current infrageneric categories of the genus Echeveria, as well as species from genera previously associated with it. The inferred consensus trees suggested that Echeveria is paraphyletic. Instead, four main clades were retrieved within the “Echeveria group”: Clade I includes exclusively Pachyphytum species. Clade II is formed by the majority of series Urbiniae; Clade III encompasses series Chloranthae, Ciliatae, Echeveria, Mucronatae, Nudae, Racemosae, Thyrsiflorae, Pachyphytum cuicatecananum and Thompsonella; Clade IV contains series Angulatae, Gibbiflorae, Occidentales, Pruinosae, Secundae, some Urbiniae species, Valvatae. genera Cremnophila, Graptopetalum and Reidmorania. Pachyphytum and Thompsonella were retrieved as monophyletic groups, but the first outside Echeveria while the latter inside. Results of our study suggest that Echeveria and the Echeveria Group require a redefinition.

A Re-analysis of the phylogeny of the genus Protobothrops (Reptilia: Viperidae), with particular reference to the systematic position of P. xiangchengensis

2006 ◽  
Vol 27 (3) ◽  
pp. 433-439 ◽  
Author(s):  
Peng Guo ◽  
Ermi Zhao ◽  
Yaping Zhang ◽  
Junfeng Pang
Keyword(s):  
Maximum Likelihood ◽  
16S Rrna ◽  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Systematic Position ◽  
Valid Species ◽  
12S Rrna

AbstractBased on three mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b), the phylogeny of Protobothrops is re-analyzed using Maximum-parsimony (MP), Maximum-likelihood (ML), and Bayesian (BI) approaches. All phylogenetic analyses indicate that all putative Protobothrops species examined formed a monophyletic group; however, the intrageneric relationships are still unresolved. The phylogenetic relationships further confirm that P. xiangchengensis is a valid species distinct from P. mucrosquamatus and that it is closely related to P. jerdonii.

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