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This hierarchy fits the actual evolutionary history of replication and development even better.
2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language).
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The analysis of each replication protein allowed us to precisely reconstruct the global evolutionary history of DNA replication in the Archaea and the dynamics that shaped this key cellular machinery from the LACA throughout the subsequent diversification of this Domain of Life.
Taken together, we provided insights into the evolutionary history of multiple replication origins in Haloarcula species, and proposed a general model of association between the dynamics of multiple replication origins and the evolution of multireplicon genome architecture in haloarchaea.
The future availability of both genomic and experimental data from a larger fraction of eukaryotic diversity will surely allow a better understanding of the diversity and evolutionary history of DNA replication in this Domain of Life.
However, the complex evolutionary history of DNA replication components and the occurrence of multiple highly divergent copies of unclear origin rendered the application of phylogenomic approaches to this cellular machinery particularly challenging.
To better understand the evolutionary history of these replication origins in haloarchaea, two distinct origin families (oriCa and oriCb, Figure 2), with the top two members excluding oriC1 in this study, were selected for further comparative analyses.
Comparison of the skew on the main chromosomes between species helps provide insight into the history of origins of replication in Hfx.
Through our precise identification and phylogenetic analysis of core replication components, we reconstructed the global evolutionary history of the DNA replication machinery in Archaea.
We argue that the significant under-represented motif pattern of CpG in an AU context - which is found in both the ssRNA viruses and innate genes, and has decreased throughout the history of H1N1 influenza replication in humans - is immunostimulatory and has been selected against during the co-evolution of viruses and host innate immune genes.
The subsequent evolutionary history of the DNA replication machinery appears very dynamic.
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