An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins

ELife
Sergio A Muñoz-GómezAndrew J Roger

Abstract

The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.

References

Aug 2, 2003·International Journal of Systematic and Evolutionary Microbiology·Jang-Cheon Cho, Stephen J Giovannoni
Mar 12, 2004·Molecular Biology and Evolution·Nicolas Lartillot, Hervé Philippe
Oct 27, 2004·Systematic Biology·Peter G Foster
Sep 17, 2005·International Journal of Systematic and Evolutionary Microbiology·Kyung-Bum LeeHiroshi Oyaizu
Jan 26, 2007·Biology Letters·Christian EsserTal Dagan
Apr 5, 2007·Nature Protocols·B Franz Lang, Gertraud Burger
May 8, 2007·Journal of Bacteriology·Kelly P WilliamsAllan W Dickerman
Jul 27, 2007·Molecular Biology and Evolution·Edward Susko, Andrew J Roger
Feb 7, 2009·International Journal of Systematic and Evolutionary Microbiology·Jutta WieseJohannes F Imhoff
Mar 28, 2009·Biology Letters·Thijs J G Ettema, Siv G E Andersson
Jun 19, 2009·Bioinformatics·Nicolas LartillotSamuel Blanquart
Sep 9, 2011·Molecular Biology and Evolution·Johan ViklundSiv G E Andersson
Dec 6, 2011·International Journal of Systematic and Evolutionary Microbiology·Timothy J WilliamsDennis A Bazylinski
Jan 25, 2012·PloS One·Martin WuJonathan A Eisen
Feb 1, 2012·PloS One·Naiara Rodríguez-Ezpeleta, T Martin Embley
Feb 23, 2012·Scientific Reports·J Cameron ThrashStephen J Giovannoni
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Sep 18, 2012·International Journal of Systematic and Evolutionary Microbiology·Dennis A BazylinskiBrian Simpson
Feb 19, 2013·Molecular Biology and Evolution·Bui Quang MinhArndt von Haeseler
Mar 20, 2013·Proceedings of the National Academy of Sciences of the United States of America·James H CampbellMircea Podar
Mar 23, 2013·Molecular Biology and Evolution·Zhang Wang, Martin Wu
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Jan 23, 2015·Scientific Reports·Zhang Wang, Martin Wu
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Oct 1, 2016·Annual Review of Marine Science·Stephen J Giovannoni

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Citations

Mar 1, 2020·MicrobiologyOpen·Mariana López-SámanoAlejandro García-de Los Santos
Sep 25, 2020·Biological Chemistry·Muriel C F van Teeseling, Martin Thanbichler
Feb 3, 2020·Cellular and Molecular Life Sciences : CMLS·István Zachar, Gergely Boza
Dec 19, 2020·Frontiers in Microbiology·Elizabeth Sage HunterChristopher E Lane
Dec 12, 2020·Computational and Structural Biotechnology Journal·Jian Jiao, Chang-Fu Tian
Feb 3, 2021·Current Opinion in Microbiology·Kathrin S Fröhlich, Manuel Velasco Gomariz
Mar 16, 2021·Open Biology·Alexei Y KostygovJulius Lukeš
May 18, 2021·Frontiers in Microbiology·Jürgen TomaschAndrew S Lang
Jun 5, 2021·Nature Communications·Sishuo Wang, Haiwei Luo
Mar 28, 2021·Genome Biology and Evolution·Tom A WilliamsT Martin Embley
Jun 3, 2021·International Journal of Molecular Sciences·Nomfundo NzuzaKhajamohiddin Syed
Jul 15, 2021·Current Biology : CB·Filip HusnikPatrick J Keeling

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Datasets Mentioned

BETA
PRJNA501864
50324
SRR8156522

Methods Mentioned

BETA
Ligation

Software Mentioned

SINA
Filtlong
chisq
IQ
BLAST
NanoLyse
RNAmmer
PhyloBayes
SiteStripper
P4

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