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Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney JO, Martin WF - Nature (2014)

Bottom Line: In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions.To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes.Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.

ABSTRACT
The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.

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Archaeal specific and import gene counts on a reference treeNumber of archaeal specific and import families corresponding to each node in the reference tree are shown in the order of ‘specific/imports’. Numbers at internal nodes indicate the number of archaeal-specific families and families with bacterial homologues that correspond to the reference tree topology. Values at the left indicate the number of archaeal-specific families and families with bacterial homologues that are present in all archaeal groups.
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Figure 10: Archaeal specific and import gene counts on a reference treeNumber of archaeal specific and import families corresponding to each node in the reference tree are shown in the order of ‘specific/imports’. Numbers at internal nodes indicate the number of archaeal-specific families and families with bacterial homologues that correspond to the reference tree topology. Values at the left indicate the number of archaeal-specific families and families with bacterial homologues that are present in all archaeal groups.

Mentions: Neither the archaea-specific genes nor the bacterial acquisitions showed evidence for any pattern of higher order archaeal relationships or hierarchical clustering20 among the 13 higher taxa, with the exception of the crenarchaeote-euryarchaeote spilt (Extended Data Fig. 6). While 16,680 gene families (14,414 archaea-specific and 2,264 acquisitions) recover the groups themselves, only 4% as many genes (601: 491 archaea-specific and 110 acquisitions) recover any branch in the reference phylogeny linking those groups (Extended Data Fig. 7).


Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney JO, Martin WF - Nature (2014)

Archaeal specific and import gene counts on a reference treeNumber of archaeal specific and import families corresponding to each node in the reference tree are shown in the order of ‘specific/imports’. Numbers at internal nodes indicate the number of archaeal-specific families and families with bacterial homologues that correspond to the reference tree topology. Values at the left indicate the number of archaeal-specific families and families with bacterial homologues that are present in all archaeal groups.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4285555&req=5

Figure 10: Archaeal specific and import gene counts on a reference treeNumber of archaeal specific and import families corresponding to each node in the reference tree are shown in the order of ‘specific/imports’. Numbers at internal nodes indicate the number of archaeal-specific families and families with bacterial homologues that correspond to the reference tree topology. Values at the left indicate the number of archaeal-specific families and families with bacterial homologues that are present in all archaeal groups.
Mentions: Neither the archaea-specific genes nor the bacterial acquisitions showed evidence for any pattern of higher order archaeal relationships or hierarchical clustering20 among the 13 higher taxa, with the exception of the crenarchaeote-euryarchaeote spilt (Extended Data Fig. 6). While 16,680 gene families (14,414 archaea-specific and 2,264 acquisitions) recover the groups themselves, only 4% as many genes (601: 491 archaea-specific and 110 acquisitions) recover any branch in the reference phylogeny linking those groups (Extended Data Fig. 7).

Bottom Line: In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions.To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes.Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.

ABSTRACT
The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.

Show MeSH