Formation of the Japanese Carabina Fauna Inferred from a Phylogenetic Tree of Mitochondrial ND5 Gene Sequences (Coleoptera, Carabidae)

2000 ◽  
Vol 50 (6) ◽  
pp. 541-549 ◽  
Author(s):  
Osamu Tominaga ◽  
Zhi-Hui Su ◽  
Choong-Gon Kim ◽  
Munehiro Okamoto ◽  
Yûki Imura ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Gene Sequences ◽  
Nd5 Gene

Phylogenetic relationships and evolution of the Japanese Carabinae ground beetles based on mitochondrial ND5 gene sequences

1996 ◽  
Vol 42 (2) ◽  
pp. 124-129 ◽  
Author(s):  
Zhi-Hui Su ◽  
Takeshi Ohama ◽  
Tokindo S. Okada ◽  
Keiko Nakamura ◽  
Ryosuke Ishikawa ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Ground Beetles ◽  
Gene Sequences ◽  
Nd5 Gene

scholarly journals Legume Symbiotic Nitrogen Fixation byβ-Proteobacteria Is Widespread inNature

2003 ◽  
Vol 185 (24) ◽  
pp. 7266-7272 ◽  
Author(s):  
Wen-Ming Chen ◽  
Lionel Moulin ◽  
Cyril Bontemps ◽  
Peter Vandamme ◽  
Gilles Béna ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nitrogen Fixation ◽  
Phylogenetic Tree ◽  
Phylogenetic Diversity ◽  
Symbiotic Nitrogen Fixation ◽  
The Other ◽  
Gene Sequences ◽  
Free Living ◽  
Initial Discovery ◽  
Different Strains

ABSTRACT Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the β-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating thatβ -proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial β-proteobacteria (β-rhizobia) are very similar to those of rhizobia from theα -subclass (α-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. Theβ -rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered β-rhizobial sequences in two nodA lineages intertwined with α-rhizobial sequences. On the other hand, theβ -rhizobia were grouped with free-living nitrogen-fixingβ -proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that β-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.

scholarly journals Analysis SARS-CoV-2 Genomes of G20 Areas on Phylogeny Tree, t-SNE based on Machine Learning

2020 ◽  
Author(s):  
Renyang Liu ◽  
Mu Qiao ◽  
Alima ◽  
Jeffrey Zheng ◽  
Wei Zhou
Keyword(s):  
Public Health ◽  
Machine Learning ◽  
Phylogenetic Tree ◽  
Treatment Strategies ◽  
Gene Sequences ◽  
Effective Prevention ◽  
Multiple Resources ◽  
The World ◽  
Prevention And Treatment ◽  
Epidemiological Characteristics

Abstract The new coronavirus disease (COVID-19) broke out earlier in Wuhan, and the plague spread rapidly from multiple resources of different countries. COVID-19 has caused millions of diagnosed people worldwide, causing many deaths and posing a severe threat to public health in countries around the world. Facing this urgent situation, in-depth research on the emerging SARS-CoV-2 to understand the related pathogenic mechanism and epidemiological characteristics is urgent. This type of activity would be useful to determine its origin to formulate effective prevention and treatment strategies for affected patients.This paper adopts t-SNE based on machine learning to draw a phylogenetic tree from collected genomic sequences to analyze G20 countries’ samples. The phylogenetic tree of the generating mechanism was described, and intermediate results were illustrated. The results of this research showed that viruses in many countries have similar or similar relationships among the gene sequences.

scholarly journals Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas

2007 ◽  
Vol 57 (9) ◽  
pp. 2037-2051 ◽  
Author(s):  
M. Martini ◽  
I.-M. Lee ◽  
K. D. Bottner ◽  
Y. Zhao ◽  
S. Botti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Ribosomal Protein ◽  
Phylogenetic Analyses ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Gram Positive ◽  
The 16S Rrna Gene

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.

Moniliella carnis sp. nov. and Moniliella dehoogii sp. nov., two novel species of black yeasts isolated from meat processing environments

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3088-3094 ◽  
Author(s):  
Vu Nguyen Thanh ◽  
Dao Anh Hai ◽  
Dinh Duc Hien ◽  
Masako Takashima ◽  
Marc-André Lachance
Keyword(s):  
Phylogenetic Tree ◽  
Type Strain ◽  
Novel Species ◽  
Large Subunit ◽  
Rrna Gene ◽  
Meat Processing ◽  
Gene Sequences ◽  
Phenotypic Characteristics ◽  
Genetic Groups ◽  
Large Subunit Rrna

Thirteen strains of yeasts typical of the genus Moniliella were isolated from fermenting meat and meat processing tools in Vietnam. PCR fingerprints generated by primer (GAC)5 subdivided the strains into two distinctive genetic groups. In a phylogenetic tree based on D1/D2 large subunit rRNA gene sequences, the strains formed a well-supported clade with Moniliella spathulata and Moniliella suaveolens but represented two new lineages. The names Moniliella carnis sp. nov. and Moniliella dehoogii sp. nov. are proposed. The two novel species can be distinguished from each other and from known species of Moniliella based on phenotypic characteristics. It is assumed that the yeasts were associated with fatty substances that contaminated the meat processing tools. The type strain of Moniliella carnis is KFP 246T ( = CBS 126447T = NRRL Y-48681T) and the type strain of Moniliella dehoogii is KFP 211T ( = CBS 126564T = NRRL Y-48682T).

scholarly journals Phylogenetic relationships in the division Lipastromorphi (Coleoptera, Carabidae) of the world as deduced from mitochondrial ND5 gene sequences

2003 ◽  
Vol 78 (1) ◽  
pp. 37-51 ◽  
Author(s):  
Zhi-Hui Su ◽  
Yûki Imura ◽  
Choong-Gon Kim ◽  
Munehiro Okamoto ◽  
Syozo Osawa
Keyword(s):  
Phylogenetic Relationships ◽  
Gene Sequences ◽  
The World ◽  
Nd5 Gene

scholarly journals Karyotype and COI gene sequence of Chironomus heteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the Gydan Peninsula, Russia

2021 ◽  
Vol 15 (4) ◽  
pp. 447-458
Author(s):  
Viktor V. Bolshakov ◽  
Alexander A. Prokin ◽  
Sergey V. Artemenko
Keyword(s):  
Phylogenetic Tree ◽  
Gene Sequence ◽  
Genetic Distances ◽  
Coi Gene ◽  
Gene Sequences ◽  
South Caucasus ◽  
Homozygous State ◽  
Banding Sequence ◽  
First Time ◽  
Georgian Population

The karyotype features and gene COI sequence of Chironomus heteropilicornis Wülker, 1996 from the Gydan Peninsula are presented for the first time. Nine banding sequences were determined, eight of them hpiA2, hpiB1, hpiC1, hpiC2, hpiD1, hpiE1, hpiF3 and hpiG1 were previously known from European, Georgian (South Caucasus) and Siberian populations. One new banding sequence for Ch. heteropilicornis, hpiB2, was found. The hpiA2 banding sequence was found in all individuals, and this is its second finding after the Georgian population (Karmokov 2019). The hpiF3 banding sequence was found only in the homozygous state. Additional B-chromosomes are absent. The genetic distances (K2P) between Ch. heteropilicornis COI gene sequence from Gydan Peninsula and Norway are 1.1­–1.3%, and Georgia – 1.8%, much lower than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. The phylogenetic tree for COI gene sequences estimated by Bayesian inference showed geographically determined clusters of Norway and Gydan and a separate lineage of the Georgian population of Ch. heteropilicornis. The analysis of karyotype and COI gene sequences shows that the population of Ch. heteropilicornis from the Gydan Peninsula has an intermediate position within the Ch. pilicornis group between Georgian, Yakutian and Norwegian populations. The position of Ch. pilicornis Fabricius, 1787 from Canada and Greenland on the phylogenetic tree is discussed.

scholarly journals Genetic analysis of mitochondrial ND5 gene of siberian ibex (Capra Sibirica, Pallas, 1776) population in Mongolia

2019 ◽  
pp. 48-53
Author(s):  
Tsenddorj Bilguun ◽  
Baatar Delgerzul ◽  
Zunduibaatar Unudbayasgalan ◽  
Baranz Galbadrakh ◽  
Batsukh Tserendulam
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Phylogenetic Tree ◽  
Central Asia ◽  
Nucleotide Diversity ◽  
Population Decline ◽  
Haplotype Diversity ◽  
Desert Steppe ◽  
Nd5 Gene ◽  
Different Parts

The Siberian ibex (Capra sibirica) from Central Asia is believed to be the most ancient species of the genus Capra. In Mongolia, it is distributed in the areas of Mongolian Altai, Gobi-Altai, Dzungaria, Altai, Khan Khuhii, Khoridal Saridag and Ulaan Taiga as well as in the desert and semi-desert steppe zones of Dundgobi and Dornogobi aimags (provinces). In the current study, we investigated the mitochondrial ND5 gene fragments of the Siberian ibex population from different parts of Mongolia. Nine haplotypes, including 6 shared and 3 unique haplotypes were identified among these populations. Furthermore, Tajima’s statistics and Fu’s statistics did not reveal significant positive value across the population, indicating population decline and balancing selection.In the phylogenetic tree by 9 haplotypes, no separated clusters were generated. In addition, nucleotide diversity was 0.015, haplotype diversity was 0.86 and the average number of differences in nucleotides was 8.2 in the overall population. These results suggest that genetic diversity across all the populations was low, while haplotype diversity and the average number of differences in nucleotides were high.

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