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 ◽  
...  
2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune

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.


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

1992 ◽  
Vol 41 (4) ◽  
pp. 483 ◽  
Author(s):  
Timothy P. Friedlander ◽  
Jerome C. Regier ◽  
Charles Mitter

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

2003 ◽  
Vol 126 (1) ◽  
pp. 119-123 ◽  
Author(s):  
Christophe Noël ◽  
Corinne Peyronnet ◽  
Delphine Gerbod ◽  
Virginia P Edgcomb ◽  
Pilar Delgado-Viscogliosi ◽  
...  

2021 ◽  
Author(s):  
David Emms ◽  
Steven Kelly

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.


2018 ◽  
Author(s):  
Mingwei Cai ◽  
Yang Liu ◽  
Zhichao Zhou ◽  
Yuchun Yang ◽  
Jie Pan ◽  
...  

AbstractAsgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.


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