Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra

Ragan, Mark A., Bernard, Guillaume and Chan, Cheong Xin (2014) Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra. RNA Biology, 11 3: 176-185. doi:10.4161/rna.27505


Author Ragan, Mark A.
Bernard, Guillaume
Chan, Cheong Xin
Title Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra
Formatted title
Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra
Journal name RNA Biology   Check publisher's open access policy
ISSN 1555-8584
1547-6286
Publication date 2014-03
Year available 2014
Sub-type Article (original research)
DOI 10.4161/rna.27505
Open Access Status DOI
Volume 11
Issue 3
Start page 176
End page 185
Total pages 10
Place of publication Austin, TX, United States
Publisher Landes Bioscience
Collection year 2015
Language eng
Formatted abstract
From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D2 statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by fulllength sequences, this stage in the development of computational molecular biology remains instructive for us today.
Keyword 16S ribosomal RNAs
K-mers
Molecular phylogenetics
Oligomers
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
Institute for Molecular Bioscience - Publications
 
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