Open Access Highly Accessed Research article

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

Arshan Nasir1, Kyung Mo Kim12 and Gustavo Caetano-Anolles1*

Author Affiliations

1 Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, IL, 61801, USA

2 Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon, 305-806, Korea

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BMC Evolutionary Biology 2012, 12:156  doi:10.1186/1471-2148-12-156

Published: 24 August 2012

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Additional file 1::

Table S1. Statistics on the assignment of FSFs in supergroups.

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Table S2. List of domain FFs that make structural components of aaRS enzymes.

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Figure S1. Universal tree of life (uToL) reconstructed from the set of universal FSFs and corresponding network tree representation. A. One optimal most parsimonious phylogenomic tree describing the evolution of 200 proteomes equally sampled from supergroups (50 each from Archaea, Bacteria, and Eukarya and viruses) generated using the census of abundance of 229 FSFs in the ABEV taxonomic group (229 parsimony informative characters; 16,642 steps; CI = 0.1302; RI = 0.8233; g1 = −0.399). Terminal leaves of viruses, Archaea, Bacteria, and Eukarya were labeled in red, blue, green, and black respectively. Numbers on the branches indicate bootstrap values. B. Network tree generated from the presence/absence matrix of 229 FSFs (228 non-constant character sites) in 200 sampled proteomes. Nodes were represented by rectangles and labeled as in A. Numbers on the major splits indicate bootstrap values. CI, consistency index; RI, retention index; g1, tree skewness.

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Figure S2. Retention index (ri) of each FSF plotted against relative age (nd). Viral FSFs are colored red as above and cellular FSFs are represented in blue. Both groups of FSFs follow an identical distribution and generally the viral FSFs are distributed with higher ri values supporting a better fit of viral characters to the phylogeny.

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