Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Qiyun Zhu; Uyen Mai; Wayne Pfeiffer; Stefan Janssen; Francesco Asnicar; Jon G. Sanders; Pedro Belda-Ferre; Gabriel A. Al-Ghalith; Evguenia Kopylova; Daniel McDonald; Tomasz Kosciolek; John B. Yin; Shi Huang; Nimaichand Salam; Jian Yu Jiao; Zijun Wu; Zhenjiang Z. Xu; Kalen Cantrell; Yimeng Yang; Erfan Sayyari; Maryam Rabiee; James T. Morton; Sheila Podell; Dan Knights; Wen Jun Li; Curtis Huttenhower; Nicola Segata; Larry Smarr; Siavash Mirarab; Rob Knight

doi:10.1038/s41467-019-13443-4

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G. Sanders, Pedro Belda-Ferre, Gabriel A. Al-Ghalith, Evguenia Kopylova, Daniel McDonald, Tomasz Kosciolek, John B. Yin, Shi Huang, Nimaichand Salam, Jian Yu Jiao, Zijun Wu, Zhenjiang Z. Xu, Kalen Cantrell, Yimeng Yang, Erfan SayyariMaryam Rabiee, James T. Morton, Sheila Podell, Dan Knights, Wen Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab, Rob Knight

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100 Scopus citations

Abstract

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Original language	English (US)
Article number	5477
Journal	Nature communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-13443-4
State	Published - Dec 1 2019
Externally published	Yes

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
General
Physics and Astronomy(all)

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10.1038/s41467-019-13443-4

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Zhu, Q., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J. G., Belda-Ferre, P., Al-Ghalith, G. A., Kopylova, E., McDonald, D., Kosciolek, T., Yin, J. B., Huang, S., Salam, N., Jiao, J. Y., Wu, Z., Xu, Z. Z., Cantrell, K., Yang, Y., ... Knight, R. (2019). Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature communications, 10(1), [5477]. https://doi.org/10.1038/s41467-019-13443-4

Zhu, Q, Mai, U, Pfeiffer, W, Janssen, S, Asnicar, F, Sanders, JG, Belda-Ferre, P, Al-Ghalith, GA, Kopylova, E, McDonald, D, Kosciolek, T, Yin, JB, Huang, S, Salam, N, Jiao, JY, Wu, Z, Xu, ZZ, Cantrell, K, Yang, Y, Sayyari, E, Rabiee, M, Morton, JT, Podell, S, Knights, D, Li, WJ, Huttenhower, C, Segata, N, Smarr, L, Mirarab, S & Knight, R 2019, 'Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea', Nature communications, vol. 10, no. 1, 5477. https://doi.org/10.1038/s41467-019-13443-4

@article{39daf403a00e455aba9a60c57158f066,

title = "Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea",

abstract = "Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.",

author = "Qiyun Zhu and Uyen Mai and Wayne Pfeiffer and Stefan Janssen and Francesco Asnicar and Sanders, {Jon G.} and Pedro Belda-Ferre and Al-Ghalith, {Gabriel A.} and Evguenia Kopylova and Daniel McDonald and Tomasz Kosciolek and Yin, {John B.} and Shi Huang and Nimaichand Salam and Jiao, {Jian Yu} and Zijun Wu and Xu, {Zhenjiang Z.} and Kalen Cantrell and Yimeng Yang and Erfan Sayyari and Maryam Rabiee and Morton, {James T.} and Sheila Podell and Dan Knights and Li, {Wen Jun} and Curtis Huttenhower and Nicola Segata and Larry Smarr and Siavash Mirarab and Rob Knight",

note = "Funding Information: We are grateful to Victor Nizet, Eric Allen, Milton Saier, J{\"u}rgen Schulze, Toni Gabald{\'o} Estevan, Benjamin Hillmann, Arturo Medrano-Soto, Madhusudan Gujral, Monika Kumaraswamy, Jeff Dereus, Anupriya Tripathi, Amnon Amir, Serene Jiang, Yoshiki V{\'a}zquez-Baeza, Thant H. Zaw for insightful discussions on this study and additional assistance. This study was supported in part by National Science Foundation grant 1565057 and the Alfred P. Sloan Foundation under grant number G-2017-9838 awarded to R.K. This work used the Comet supercomputer at the San Diego Supercomputer Center through allocation BIO150043, awarded to R.K., L.S. and S.M. through the Extreme Science and Engineering Discovery Environment (XSEDE). Both Comet and XSEDE are funded by the National Science Foundation. S.M., U.M., and M.R. were supported by the National Science Foundation grant III-1845967 to S.M. W.L. was supported by National Natural Science Foundation of China (91951205). Publisher Copyright: {\textcopyright} 2019, The Author(s).",

year = "2019",

month = dec,

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doi = "10.1038/s41467-019-13443-4",

language = "English (US)",

volume = "10",

journal = "Nature Communications",

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TY - JOUR

T1 - Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

AU - Zhu, Qiyun

AU - Mai, Uyen

AU - Pfeiffer, Wayne

AU - Janssen, Stefan

AU - Asnicar, Francesco

AU - Sanders, Jon G.

AU - Belda-Ferre, Pedro

AU - Al-Ghalith, Gabriel A.

AU - Kopylova, Evguenia

AU - McDonald, Daniel

AU - Kosciolek, Tomasz

AU - Yin, John B.

AU - Huang, Shi

AU - Salam, Nimaichand

AU - Jiao, Jian Yu

AU - Wu, Zijun

AU - Xu, Zhenjiang Z.

AU - Cantrell, Kalen

AU - Yang, Yimeng

AU - Sayyari, Erfan

AU - Rabiee, Maryam

AU - Morton, James T.

AU - Podell, Sheila

AU - Knights, Dan

AU - Li, Wen Jun

AU - Huttenhower, Curtis

AU - Segata, Nicola

AU - Smarr, Larry

AU - Mirarab, Siavash

AU - Knight, Rob

N1 - Funding Information: We are grateful to Victor Nizet, Eric Allen, Milton Saier, Jürgen Schulze, Toni Gabaldó Estevan, Benjamin Hillmann, Arturo Medrano-Soto, Madhusudan Gujral, Monika Kumaraswamy, Jeff Dereus, Anupriya Tripathi, Amnon Amir, Serene Jiang, Yoshiki Vázquez-Baeza, Thant H. Zaw for insightful discussions on this study and additional assistance. This study was supported in part by National Science Foundation grant 1565057 and the Alfred P. Sloan Foundation under grant number G-2017-9838 awarded to R.K. This work used the Comet supercomputer at the San Diego Supercomputer Center through allocation BIO150043, awarded to R.K., L.S. and S.M. through the Extreme Science and Engineering Discovery Environment (XSEDE). Both Comet and XSEDE are funded by the National Science Foundation. S.M., U.M., and M.R. were supported by the National Science Foundation grant III-1845967 to S.M. W.L. was supported by National Natural Science Foundation of China (91951205). Publisher Copyright: © 2019, The Author(s).

PY - 2019/12/1

Y1 - 2019/12/1

N2 - Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

AB - Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

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SN - 2041-1723

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JO - Nature Communications

JF - Nature Communications

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ER -

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

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