An integrated phylogenomic approach toward pinpointing the origin of mitochondria

Scientific Reports
Zhang Wang, Martin Wu

Abstract

Overwhelming evidence supports the endosymbiosis theory that mitochondria originated once from the Alphaproteobacteria. However, its exact position in the tree of life remains highly debated. This is because systematic errors, including biased taxonomic sampling, high evolutionary rates and sequence composition bias have long plagued the mitochondrial phylogenetics. In this study, we address this issue by 1) increasing the taxonomic representation of alphaproteobacterial genomes by sequencing 18 phylogenetically novel species. They include 5 Rickettsiales and 4 Rhodospirillales, two orders that have shown close affiliations with mitochondria previously, 2) using a set of 29 slowly evolving mitochondria-derived nuclear genes that are less biased than mitochondria-encoded genes as the alternative "well behaved" markers for phylogenetic analysis, 3) applying site heterogeneous mixture models that account for the sequence composition bias. With the integrated phylogenomic approach, we are able to for the first time place mitochondria unequivocally within the Rickettsiales order, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. Our results suggest that mitochondria most...Continue Reading

References

Apr 9, 1981·Nature·S AndersonI G Young
Jan 1, 1995·Molecular Biology and Evolution·G M LentoD Penny
Mar 21, 1994·FEBS Letters·A M Viale, A K Arakaki
Jun 2, 1994·Nature·D M HillisD L Swofford
Jan 7, 1993·Nature·M Hasegawa, T Hashimoto
Mar 24, 1998·Nature·W Martin, M Müller
Mar 5, 1999·Science·M W GrayB F Lang
Mar 27, 1999·Journal of Molecular Evolution·P G Foster, D A Hickey
Aug 26, 1999·The Journal of Eukaryotic Microbiology·B F LangG Burger
Nov 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·K L AdamsJ D Palmer
Oct 12, 2000·Yeast·O KarlbergS G Andersson
Oct 12, 2000·Proceedings of the National Academy of Sciences of the United States of America·S Karlin, L Brocchieri
Dec 6, 2000·Microbiology and Molecular Biology Reviews : MMBR·C G Kurland, S G Andersson
Feb 13, 2001·Trends in Ecology & Evolution·P J. Lockhart, S A. Cameron
Jun 26, 2001·Genome Biology·M W GrayB F Lang
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Feb 5, 2003·Molecular Phylogenetics and Evolution·Kendall D ClementsJ Howard Choat
Feb 22, 2003·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Siv G E AnderssonCharles G Kurland
Apr 16, 2003·European Journal of Biochemistry·Victor V Emelyanov
Aug 2, 2003·Science·Toni Gabaldón, Martijn A Huynen
Dec 3, 2003·Trends in Genetics : TIG·Gertraud BurgerB Franz Lang
Mar 12, 2004·Molecular Biology and Evolution·Nicolas Lartillot, Hervé Philippe
Apr 16, 2004·Molecular Biology and Evolution·Matthew J PhillipsDavid Penny
Sep 30, 2004·BMC Evolutionary Biology·Sasa StefanovićJeffrey D Palmer
Feb 11, 2005·Molecular Biology and Evolution·Hervé PhilippeHenner Brinkmann
Apr 30, 2005·Nature Reviews. Genetics·Frédéric DelsucHervé Philippe
May 11, 2005·Trends in Plant Science·Peter J Lockhart, David Penny
Jun 10, 2005·Molecular Biology and Evolution·Jim Leebens-MackClaude W depamphilis
Jul 30, 2005·Systematic Biology·Mike Steel
Oct 14, 2005·Molecular Biology and Evolution·Daniel H Huson, David Bryant
Oct 26, 2005·Systematic Biology·Henner BrinkmannHervé Philippe
Feb 24, 2006·Trends in Genetics : TIG·Olivier JeffroyHervé Philippe
Jan 24, 2007·Bioinformatics·Arthur L DelcherSteven L Salzberg
May 8, 2007·Journal of Bacteriology·Kelly P WilliamsAllan W Dickerman

❮ Previous
Next ❯

Citations

Jun 23, 2015·Molecular Microbiology·Soraya Aït-Bara, Agamemnon J Carpousis
Apr 25, 2015·Environmental Microbiology·Frederik SchulzMatthias Horn
Sep 2, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Tom A Williams, T Martin Embley
Apr 8, 2015·Proceedings of the National Academy of Sciences of the United States of America·Michael W Gray
Sep 4, 2015·PloS One·Daniel S CarvalhoCharbel N El-Hani
Oct 1, 2016·Annual Review of Marine Science·Stephen J Giovannoni
Apr 28, 2017·Clinical Toxicology : the Official Journal of the American Academy of Clinical Toxicology and European Association of Poisons Centres and Clinical Toxicologists·Eike BlohmMark Neavyn
Apr 27, 2017·Molecular Biology and Evolution·Andrea PozziMarco Passamonti
Aug 22, 2017·International Journal of Molecular Sciences·Erzsébet Bartolák-SukiBéla Suki
Apr 17, 2018·Genome Biology and Evolution·Anna M FlorianoDavide Sassera
Nov 11, 2017·Nature Reviews. Microbiology·Laura EmeThijs J G Ettema
Dec 19, 2017·Virus Evolution·Migun ShakyaOlga Zhaxybayeva
Dec 9, 2015·American Journal of Botany·David A Baum
Nov 14, 2018·Acta Biochimica Et Biophysica Sinica·Le ChangJianhua Li
Nov 28, 2017·Nature Reviews. Microbiology·Filip Husnik, John P McCutcheon
Aug 2, 2019·PloS One·Oliver Vickman, Albert Erives
May 28, 2016·Science·Steven G BallAndreas P M Weber
Feb 26, 2016·Science·Steven G BallAndreas P M Weber
Mar 19, 2020·Cellular Microbiology·Fabrizia StavruDavide Sassera
Jun 4, 2020·Biochemical Society Transactions·Luis Alberto Luévano-Martínez, Anna L Duncan
Jun 25, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Karolina BoguszewskaBolesław T Karwowski
Jun 1, 2018·BMC Genomics·Behrooz DarbaniIrina Borodina
Jul 30, 2019·Frontiers in Microbiology·Kelsey R MooreGregory P Fournier
Jun 4, 2020·International Journal of Molecular Sciences·Hector MendozaJan Schirawski
Jan 31, 2020·Frontiers in Genetics·Dan MishmarNeal Sondheimer
Sep 1, 2017·The New Phytologist·Juliet BrodieDebashish Bhattacharya
Sep 18, 2017·Journal of Biomedical Science·Tzu-Yu WengTsung-Ping Su
Apr 27, 2018·Nature·Joran MartijnThijs J G Ettema
Jan 23, 2018·Frontiers in Medicine·Louise C Kenny, Douglas B Kell
Apr 28, 2019·International Journal of Molecular Sciences·Steffi GoffartJaakko L O Pohjoismäki
Jun 9, 2020·Redox Biology·Jamelle A BrownScott W Ballinger
Apr 1, 2017·Mitochondrial DNA. Part B, Resources·Przemysław GagatPaweł Mackiewicz

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Methods Mentioned

BETA
whole-genome shotgun sequencing
Illumina sequencing

Software Mentioned

AMPHORA
nh
phylobayes
GLIMMER
FastTree
AMPHORA2
Split Analyses Methods ( SAMS )
RAxML
SplitsTree
ZORRO

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