Phylogenetic Analysis of Perkinsus Based on Actin Gene Sequences

1997 ◽  
Vol 83 (3) ◽  
pp. 417 ◽  
Author(s):  
Kimberly S. Reece ◽  
Mark E. Siddall ◽  
Eugene M. Burreson ◽  
John E. Graves
Keyword(s):  
Phylogenetic Analysis ◽  
Actin Gene ◽  
Gene Sequences

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

Nuclear Gene Sequences for Higher Level Phylogenetic Analysis: 14 Promising Candidates

1992 ◽  
Vol 41 (4) ◽  
pp. 483 ◽  
Author(s):  
Timothy P. Friedlander ◽  
Jerome C. Regier ◽  
Charles Mitter
Keyword(s):  
Phylogenetic Analysis ◽  
Nuclear Gene ◽  
Gene Sequences

scholarly journals Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class polyacanthocephala (acanthocephala)

2002 ◽  
Vol 23 (2) ◽  
pp. 288-292 ◽  
Author(s):  
Martı́n Garcı́a-Varela ◽  
Michael P Cummings ◽  
Gerardo Pérez-Ponce de León ◽  
Scott L Gardner ◽  
Juan P Laclette
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Rna ◽  
Gene Sequences ◽  
Ribosomal Rna Gene ◽  
18S Ribosomal Rna ◽  
18S Ribosomal Rna Gene

Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences

2003 ◽  
Vol 126 (1) ◽  
pp. 119-123 ◽  
Author(s):  
Christophe Noël ◽  
Corinne Peyronnet ◽  
Delphine Gerbod ◽  
Virginia P Edgcomb ◽  
Pilar Delgado-Viscogliosi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Gene Sequences ◽  
Small Subunit Rrna Gene

Trypanosoma rangeli isolates of bats from Central Brazil: Genotyping and phylogenetic analysis enable description of a new lineage using spliced-leader gene sequences

Acta Tropica ◽  
2009 ◽  
Vol 109 (3) ◽  
pp. 199-207 ◽  
Author(s):  
F. Maia da Silva ◽  
A. Marcili ◽  
L. Lima ◽  
M. Cavazzana ◽  
P.A. Ortiz ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Sequences ◽  
Trypanosoma Rangeli ◽  
Spliced Leader ◽  
Central Brazil

scholarly journals Structure, expression and phylogenetic analysis of the gene encoding actin I in Pneumocystis carinii.

Genetics ◽  
1994 ◽  
Vol 137 (3) ◽  
pp. 743-750 ◽  
Author(s):  
L D Fletcher ◽  
J M McDowell ◽  
R R Tidwell ◽  
R B Meagher ◽  
C C Dykstra
Keyword(s):  
Phylogenetic Analysis ◽  
Essential Gene ◽  
Pneumocystis Carinii ◽  
Comparative Sequence Analysis ◽  
Cdna Clones ◽  
Actin Gene ◽  
Gene Encoding ◽  
Actin Protein ◽  
Relationship Of ◽  
High Degree

Abstract Actin is a major component of the cytoskeleton and one of the most abundant proteins found in eukaryotic cells. Comparative sequence analysis shows that this essential gene has been highly conserved throughout eukaryotic evolution making it useful for phylogenetic analysis. Complete cDNA clones for the actin-encoding gene were isolated and characterized from Pneumocystis carinii purified from immunosuppressed rat lungs. The nucleotide sequence encodes a protein of 376 amino acids. The predicted actin protein of P. carinii shares a high degree of conservation to other known actins. Only one major actin gene was found in P. carinii. The P. carinii actin sequence was compared with 30 other actin sequences. Gene phylogenies constructed using both neighbor-joining and protein parsimony methods places the P. carinii actin sequence closest to the majority of the fungi. Since the phylogenetic relationship of P. carinii to fungi and protists has been questioned, these data on the actin gene phylogeny support the grouping of P. carinii with the fungi.

scholarly journals SHOOT: phylogenetic gene search and ortholog inference

2021 ◽  
Author(s):  
David Emms ◽  
Steven Kelly
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Trees ◽  
Query Sequence ◽  
Gene Tree ◽  
Biological Research ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Gene Search

Determining the evolutionary relationships between gene sequences is fundamental to comparative biological research. However, conducting such analyses requires a high degree of technical proficiency in several computational tools including gene family construction, multiple sequence alignment, and phylogenetic inference. Here we present SHOOT, an easy to use phylogenetic search engine for fast and accurate phylogenetic analysis of biological sequences. SHOOT searches a user-provided query sequence against a database of phylogenetic trees of gene sequences (gene trees) and returns a gene tree with the given query sequence correctly grafted within it. We show that SHOOT can perform this search and placement with comparable speed to a conventional BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional multiple sequence alignment and maximum likelihood tree inference approaches. We further show that SHOOT can be used to identify orthologs with equivalent accuracy to conventional orthology inference methods. In summary, SHOOT is an accurate and fast tool for complete phylogenetic analysis of novel query sequences. An easy to use webserver is available online at www.shoot.bio.

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