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

Biotechnology Institute

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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

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© 2019, The Author(s).

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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), Article 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

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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.",

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AU - Belda-Ferre, Pedro

AU - Al-Ghalith, Gabriel A.

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AU - McDonald, Daniel

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AU - Yin, John B.

AU - Huang, Shi

AU - Salam, Nimaichand

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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

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

Abstract

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