Open Access Research article

Massive expansion of the calpain gene family in unicellular eukaryotes

Sen Zhao1, Zhe Liang2, Viktor Demko2, Robert Wilson3, Wenche Johansen3, Odd-Arne Olsen23 and Kamran Shalchian-Tabrizi1*

  • * Corresponding author: Kamran Shalchian-Tabrizi kamran@bio.uio.no

  • † Equal contributors

Author Affiliations

1 Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, OSLO, N-0136, Norway

2 Norwegian University of Life Sciences, Ås, N-1432, Norway

3 Hedmark University College, Hamar, N-2306, Norway

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BMC Evolutionary Biology 2012, 12:193  doi:10.1186/1471-2148-12-193

Published: 29 September 2012

Additional files

Additional file 1:

Table S1. Accession numbers, domain combination of calpains.

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Additional file 2:

Figure S1. Eukaryotic calpain phylogeny inferred from the CysPc domain alignment (247 calpain sequences and 202 positions). The phylogeny is obtained from the consensus between two independent Bayesian inferences. For each node, support values are marked (numbers from left to right: Bayesian posterior probabilities (PP) inferred under LG /CAT models and maximum-likelihood bootstraps (% BP) inferred using PROTGAMMALG model) if all are more than 80% BP and 0.8 PP (filled circle) or more than 50% BP and 0.5 PP (open circle). Dashes ‘-’ show the support values are marked< 50% BP or 0.5 PP. For multiple CysPc domains found in the calpain sequence,1st, 2nd and 3rd indicate their orders from N-terminus to C-terminus of the calpain sequence. The domains marked by ‘*’ indicate their identities only have marginal significance of e-value in domain database research due to high sequence divergence. The branches and clades are assigned to the numbers that represent specified domain combinations shown in Figure 1.

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Additional file 3:

Figure S2. Eukaryotic calpain phylogeny rooted by the bacterial outgroup (246 eukaryotic + 15 prokaryotic calpain sequences; 202 positions). The phylogeny is obtained from the consensus between two independent Bayesian inferences. For each node, support values are marked (numbers from left to right: Bayesian posterior probabilities (PP) inferred under LG (left) /CAT (middle) models and maximum-likelihood bootstraps (% BP) inferred using PROTGAMMALG (right) model) if all are more than 80% BP and 0.8 PP (filled circle) or more than 50% BP and 0.5 PP (open circle). Dashes ‘-’ show the support values < 50% BP or 0.5 PP. For multiple CysPc domains found in the calpain sequence,1st, 2nd and 3rd indicate their orders from N-terminus to C-terminus of the calpain sequence. The domains marked by ‘*’ indicate their identities only have marginal significance of e-value in domain database research due to high sequence divergence. The branches and clades are assigned to the numbers that represent specified domain combinations shown in Figure 1. The alignment used to build this phylogeny can be downloaded from http://www.mn.uio.no/bio/english/people/aca/kamran/data/Calpain_final_261_accession_outgroup.dat. webcite

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Additional file 4:

Figure S3. Phylogeny of the calpain genes with MIT modules. The tree is obtained from the consensus between two independent Bayesian inferences. Support values are marked at the nodes, and numbers from left to right represent Bayesian posterior probabilities (PP) inferred under CAT /LG models and the maximum-likelihood bootstraps (% BP) inferred using PROTGAMMALG model in RAxML v7.2.5. All support values more than 80% BP and 0.8 PP or more than 50% BP and 0.5 PP are shown as full or open circles. Dashes ‘-’ show the support values < 50% or 0.5 PP. The MIT calpain genes found in Tetraodon nigroviridis, Takifugu rubripes, Gasterosteus aculeatus, Gadus morhua, Salmo salar, Danio rerio, Oryzia latipes, Gallus gallus, Dasypus novemcinctus, Ailuropoda melanoleuca, Sus scrofa, Canis familiaris, Bos taurus and Rattus norvegicus are added to this analysis. The domains marked by ‘*’ indicate their identities only have marginal significance of e-value in domain database research due to high sequence divergence. The branches and clades are assigned to the numbers that correspond to specified domain combinations shown in Figure 1. The alignment used to reconstruct the phylogeny of MIT calpains can be downloaded from http://www.mn.uio.no/bio/english/people/aca/kamran/data/Calpain_MIT_accession.dat. webcite

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Additional file 5:

Figure S4. Proposed origin of calpain superfamily domain combinations shown on the global eukaryote phylogeny. The tree is rooted according to Cavalier-Smith T 2010. Biol Lett 6(3):342-345. Red bars on the branches indicate the hypothetical origin of specified domain combinations. Calpain variants only found in one taxon or among closely related species are marked in red within the supergroup rectangles, which likely constitute lineage-specific domain combinations.

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Additional file 6:

Figure S5. Phylogeny of calpains in Metazoa. The topology is obtained from the consensus between two independent Bayesian inferences. The representative taxa sampled here include Homo species, Mus musculus, Gallus gallus, Xenopus laevis, Danio rerio, Nematostella vectensis, Drosophila melanogaster, Caenorhabditis elegans, Trichoplas adhaerens and Amphimedon queenslandica. Support values are marked at the nodes, and number from left to right represent Bayesian posterior probabilities (PP) inferred under CAT /LG models and the maximum-likelihood bootstraps (% BP) inferred using PROTGAMMALG model. All support values more than 80% BP and 0.8 PP or more than 50% BP and 0.5 PP are marked by full or open circles. Dashes ‘-’ indicate the support values < 50% BP or 0.5 PP. The branches and clades are assigned to the numbers that represent specified domain combinations listed in Figure 1. The alignment used to construct this phylogeny can be downloaded from http://www.mn.uio.no/bio/english/people/aca/kamran/data/Calpain_Metazoa_accession.dat. webcite

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