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. 2013 Apr 10:14:240.
doi: 10.1186/1471-2164-14-240.

Reevaluation of the evolutionary events within recA/RAD51 phylogeny

Sree V Chintapalli  1 , Gaurav Bhardwaj, Jagadish Babu, Loukia Hadjiyianni, Yoojin Hong, George K Todd, Casey A Boosalis, Zhenhai Zhang, Xiaofan Zhou, Hong Ma, Andriy Anishkin, Damian B van Rossum, Randen L Patterson
Affiliations

Reevaluation of the evolutionary events within recA/RAD51 phylogeny

Sree V Chintapalli et al. BMC Genomics. .

Abstract

Background: The recA/RAD51 gene family encodes a diverse set of recombinase proteins that affect homologous recombination, DNA-repair, and genome stability. The recA gene family is expressed across all three domains of life - Eubacteria, Archaea, and Eukaryotes - and even in some viruses. To date, efforts to resolve the deep evolutionary origins of this ancient protein family have been hindered by the high sequence divergence between paralogous groups (i.e. ~30% average pairwise identity).

Results: Through large taxon sampling and the use of a phylogenetic algorithm designed for inferring evolutionary events in highly divergent paralogs, we obtained a robust, parsimonious and more refined phylogenetic history of the recA/RAD51 superfamily.

Conclusions: In summary, our model for the evolution of recA/RAD51 family provides a better understanding of the ancient origin of recA proteins and the multiple events that lead to the diversification of recA homologs in eukaryotes, including the discovery of additional RAD51 sub-families.

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Figures

Figure 1
Figure 1
Distribution and Characterization of PHYRN-Derived Phylogenetic Signal in recA/RAD51 Superfamily. (A) Distribution of PHYRN Phylogenetic signal (%identity x %coverage) for recA/RAD51 superfamily. PHYRN score is calculated from alignments between full length query sequences and the respective recA/RAD51-specific PSSM library. PHYRN scores are represented as log-scaled values ranging from 0 (blue) to 4 (red). (B) Graphical representation of PHYRN phylogenetic signal of recA/RAD51 sequences (signal) as compared to their randomized versions (i.e. noise, 100 replicates). Comparative analysis is represented as Difference Ratio (DR).
Figure 2
Figure 2
Phylogenetic Inference of the recA/RAD51 Superfamily using PHYRN-NJ. (A) Unrooted phylogram of recA/RAD51 clades of Set-1 of 545 sequences. (B) Unrooted phylogram of recA/RAD51 clades of Set-2 of 633 sequences (comprising of Set-1 + 88 metagenomic sequences). Confidence values are calculated by Jackknife resampling for 5000 replicates for both the sets. Scale bar is proportional to PHYRN-derived Euclidean distance scaled between 0-1.
Figure 3
Figure 3
Evolution of recA sequences. (A) A phylogenetic tree of 242 recA sequences inferred using PHYRN-NJ and rooted with Spirochaetes. Branch statistics are derived from Jacknife resampling tests. The notation (-) is indicative of no support for the given branching pattern. Scale bar is proportional to PHYRN-derived Euclidean distance scaled between 0–1.
Figure 4
Figure 4
Model of the Evolutionary History of the recA/RAD51 Superfamily. Graphical representation of a model for evolution of recA/RAD51 family based on the phylogenetic trees obtained using PHYRN methodology. Endosymbiotic gene transfer events from cyanobacteria to protists and algae to plants are labeled. (*) represents Meiosis specific gene.
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