Population genetics and phylogenetic analysis of Colorado Borrelia burgdorferi.

1999 ◽  
Vol 60 (4) ◽  
pp. 699-707 ◽  
Author(s):  
D E Norris ◽  
J L Clark ◽  
W C Black ◽  
B J Johnson ◽  
G O Maupin ◽  
...  
Keyword(s):  
Population Genetics ◽  
Phylogenetic Analysis ◽  
Borrelia Burgdorferi

Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley

Genome ◽  
2014 ◽  
Vol 57 (4) ◽  
pp. 239-244 ◽  
Author(s):  
Xifeng Ren ◽  
Yonggang Wang ◽  
Songxian Yan ◽  
Dongfa Sun ◽  
Genlou Sun
Keyword(s):  
Population Genetics ◽  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Hordeum Vulgare ◽  
Nucleotide Diversity ◽  
Wild Barley ◽  
Haplotype Diversity ◽  
Lateral Spikelet ◽  
Cultivated Barley ◽  
Barley Population

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

scholarly journals Analysis of 46,046 SARS-CoV-2 whole-genomes leveraging principal component analysis (PCA)

2020 ◽  
Author(s):  
Christiane Scherer ◽  
James Grover ◽  
Darby Kammeraad ◽  
Gabe Rudy ◽  
Andreas Scherer
Keyword(s):  
Principal Component Analysis ◽  
Population Genetics ◽  
Phylogenetic Analysis ◽  
Principal Component ◽  
Large Data ◽  
Component Analysis ◽  
Comprehensive Analysis ◽  
Large Data Sets ◽  
Data Sets ◽  
Whole Genomes

AbstractSince the beginning of the global SARS-CoV-2 pandemic, there have been a number of efforts to understand the mutations and clusters of genetic lines of the SARS-CoV-2 virus. Until now, phylogenetic analysis methods have been used for this purpose. Here we show that Principal Component Analysis (PCA), which is widely used in population genetics, can not only help us to understand existing findings about the mutation processes of the virus, but can also provide even deeper insights into these processes while being less sensitive to sequencing gaps. Here we describe a comprehensive analysis of a 46,046 SARS-CoV-2 genome sequence dataset downloaded from the GISAID database in June of this year.SummaryPCA provides deep insights into the analysis of large data sets of SARS-CoV-2 genomes, revealing virus lineages that have thus far been unnoticed.

scholarly journals Borrelia Isolates in Northern Colorado Identified as Borrelia bissettii

2000 ◽  
Vol 38 (8) ◽  
pp. 3103-3105 ◽  
Author(s):  
Bradley S. Schneider ◽  
Nordin S. Zeidner ◽  
Thomas R. Burkot ◽  
Gary O. Maupin ◽  
Joseph Piesman
Keyword(s):  
Phylogenetic Analysis ◽  
Borrelia Burgdorferi ◽  
Intergenic Spacer ◽  
Sensu Stricto ◽  
Ribosomal Genes ◽  
Northern Colorado

Previous work described Borrelia burgdorferi sensu lato group DN127 as a new genospecies, Borrelia bissettii, and prompted the present study to identify the Borrelia spp. that exist in northern Colorado. To determine the genospecies present, we analyzed two specific intergenic spacer regions located between the 5S and 23S and the 16S and 23S ribosomal genes. Phylogenetic analysis of the derived sequences clearly demonstrated that these isolates, originating from rodents captured in the foothills of northern Colorado, diverged from B. burgdorferi sensu stricto by 5 to 5.5% and were members of the new genospecies B. bissettii.

scholarly journals Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato

2011 ◽  
Vol 11 (7) ◽  
pp. 1545-1563 ◽  
Author(s):  
Gabriele Margos ◽  
Stephanie A. Vollmer ◽  
Nicholas H. Ogden ◽  
Durland Fish
Keyword(s):  
Population Genetics ◽  
Borrelia Burgdorferi ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Phylogeny And Evolution

scholarly journals Horizontally Acquired Genes for Purine Salvage in Borrelia spp. Causing Relapsing Fever

2005 ◽  
Vol 73 (9) ◽  
pp. 6165-6168 ◽  
Author(s):  
Alan G. Barbour ◽  
Adrienne D. Putteet-Driver ◽  
Jonas Bunikis
Keyword(s):  
Phylogenetic Analysis ◽  
Borrelia Burgdorferi ◽  
Evolutionary History ◽  
Rrna Genes ◽  
Borrelia Miyamotoi ◽  
Salvage Pathway ◽  
Relapsing Fever ◽  
Purine Salvage ◽  
Borrelia Hermsii

ABSTRACT Unlike Borrelia burgdorferi, the relapsing fever agent Borrelia hermsii and the related Borrelia miyamotoi had purA and purB genes of the purine salvage pathway. These were located among the rRNA genes. Phylogenetic analysis indicated that these genes had a different evolutionary history than those of orthologs in other spirochetes.

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