Open Access Research article

Reevaluation of the evolutionary events within recA/RAD51 phylogeny

Sree V Chintapalli13, Gaurav Bhardwaj23, Jagadish Babu45, Loukia Hadjiyianni3, Yoojin Hong46, George K Todd17, Casey A Boosalis17, Zhenhai Zhang4, Xiaofan Zhou8, Hong Ma8, Andriy Anishkin4, Damian B van Rossum45* and Randen L Patterson123*

Author Affiliations

1 Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, USA

2 Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, USA

3 Center for Translational Bioscience and Computing, University of California, Davis, USA

4 Center for Computational Proteomics, The Pennsylvania State University, Pennsylvania, USA

5 Department of Biology, The Pennsylvania State University, Pennsylvania, USA

6 Department of Computer Science and Engineering, The Pennsylvania State University, Pennsylvania, USA

7 Molecular, Cellular and Integrative Physiology Graduate Group, University of California, Davis, USA

8 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania, USA

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BMC Genomics 2013, 14:240  doi:10.1186/1471-2164-14-240

Published: 10 April 2013

Additional files

Additional file 1: Figure S1:

Phylogenetic Inference of the recA/RAD51 Superfamily using MSA-based methods. Representative phylogenetic trees of recA/RAD51 gene family as inferred in (A) Lin et al. (2006) and (B) Wu et al. (2011). Clades with metagenomic sequences that are unique to Wu et al. are demarcated in red. The notation (-) is indicative of no support for the given branching pattern.

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Additional file 2: Figure S2:

Uncollapsed PHYRN tree of 545-recA/RAD51 sequences (Set-1). Phylogram of 545 recA/RAD51 sequences as inferred using PHYRN. Euclidean distance was calculated using a 545 x 545 composite score matrix, and trees were calculated from Euclidean distance matrix using Neighbor-Joining (NJ) algorithm. Confidence values were calculated using Jacknife resampling of 5000 replicates, wherein 80% of the matrix was subsampled for each replicate.

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Additional file 3: Figure S3:

Uncollapsed PHYRN tree of 633-recA/RAD51 sequences (Set-2). Phylogram of 633 recA/RAD51 sequences as inferred using PHYRN. Euclidean distance was calculated using a 633 x 633 composite score matrix, and trees were calculated from Euclidean distance matrix using Neighbor-Joining (NJ) algorithm. Confidence values were calculated using Jacknife resampling of 5000 replicates, wherein 80% of the matrix was subsampled for each replicate. [The metagenomic sequences added in 6 new groups have retained the same ID numbers presented in Wu et. al. (ID15- Unknown 1, ID2- Phage SAR1, ID5-Phage SAR2, ID4-Phage UvsX, ID11-recA-SAR1 and ID9-Unknown 2)].

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Additional file 4: Figure S4:

Phylogenetic Inference of recA/RAD51 protein family inferred using MUSCLE-NJ. Phylogenetic tree of 633 recA/RAD51 sequences as inferred using MUSCLE-NJ. Optimal MSA was obtained using MUSCLE. Protdist from PHYLIP v 3.9 was used to calculate distance matrix with JTT as substitution matrix of choice, and gamma value of 0.8. Confidence values were calculated using Bootstrap resampling method with 1000 replicates.

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Additional file 5: Figure S5:

Collapsed MUSCLE-RaxML tree of 633-recA/RAD51 sequences.Phylogenetic tree of 633 recA/RAD51 sequences as inferred using MUSCLE-RaxML. Optimal MSA was obtained using MUSCLE. Protdist from PHYLIP v 3.9 was used to calculate distance matrix with JTT as substitution matrix of choice, and gamma value of 0.8. Confidence values were calculated using Bootstrap resampling method with 1000 replicates.

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