Amplification and sequencing of variable regions in bacterial 23S ribosomal RNA genes with conserved primer sequences

1993 ◽  
Vol 27 (3) ◽  
pp. 147-151 ◽  
Author(s):  
Guy Van Camp ◽  
Sabine Chapelle ◽  
Rupert De Wachter
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Rna Genes ◽  
Variable Regions ◽  
23S Ribosomal Rna ◽  
Rna Genes

scholarly journals K-mer similarity, networks of microbial genomes and taxonomic rank

2017 ◽  
Author(s):  
Guillaume Bernard ◽  
Paul Greenfield ◽  
Mark A. Ragan ◽  
Cheong Xin Chan
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Trees ◽  
Ribosomal Rna Genes ◽  
Taxonomic Rank ◽  
Variable Regions ◽  
Microbial Life ◽  
New Perspective ◽  
Genomic Regions ◽  
The Impact ◽  
Rna Genes

AbstractAlignment-free (AF) methods have recently been adopted to infer phylogenetic trees. However, the evolutionary relationships among microbes, impacted by common phenomena such as lateral genetic transfer and rearrangement, cannot be adequately captured in a strictly tree-like structure. Bacterial and archaeal genomes consist of highly conserved regions, e.g. ribosomal RNA genes (commonly used as phylogenetic markers), more-variable regions and extrachromosomal elements, i.e. plasmids (that contain genes critical under a selective condition e.g. antibiotic resistance). The impact of these elements on genome-scale inference of microbial phylogeny remains little known. Here, using an AF approach, we inferred phylogenomic networks of microbial life based on 2785 completely sequenced bacterial and archaeal genomes, and systematically assessed the impact of ribosomal RNA genes and plasmid sequences in this network. Our results indicate that k-mer similarity can correlate with taxonomic rank of microbes. Using a relational database approach, we linked the implicatedk-mers to annotated genomic regions (thus functions), and defined core functions in specific phyletic groups and genera. We found that, in most phyla, highly conserved functions are often related to Amino acid metabolism and transport, and Energy production and conversion. Our findings indicate that AF phylogenomics can be used to infer reticulate relationships in a scalable manner and provide new perspective into microbial biology and evolution.

A Molecular Approach to the Phylogeny of Bryophytes: Cladistic Analysis of Chloroplast-Encoded 16S and 23S Ribosomal RNA Genes

1992 ◽  
Vol 95 (2) ◽  
pp. 172 ◽  
Author(s):  
Brent D. Mishler ◽  
Peter H. Thrall ◽  
John S. Hopple ◽  
Efrain De Luna ◽  
Rytas Vilgalys
Keyword(s):  
Ribosomal Rna ◽  
Cladistic Analysis ◽  
Ribosomal Rna Genes ◽  
Molecular Approach ◽  
23S Ribosomal Rna ◽  
Rna Genes
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