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Open Access Research article

The evolution of cardiolipin biosynthesis and maturation pathways and its implications for the evolution of eukaryotes

Hai-Feng Tian12, Jin-Mei Feng12 and Jian-Fan Wen1*

Author Affiliations

1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province 650223, China

2 Graduate School of the Chinese Academy of Sciences, Beijing 100039, China

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BMC Evolutionary Biology 2012, 12:32  doi:10.1186/1471-2148-12-32

Published: 13 March 2012

Additional files

Additional file 1:

Additional file 1. Identified homologs involved in CLS synthesis and maturation pathways in eukaryotes.

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Additional file 2:

Figure S1. The alignment of CLS_cap of eukaryotes (part). Conserved six membrane-binding regions are designated as I-VI and conserved amino acid residues among CAP family are boxed. Amino acid positions are numbered relative to the Monosiga brevicollis ortholog. # below the alignment indicates the amino acid residues that are specific for CL synthases.

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Additional file 3:

Figure S2. The identified conserved motifs (the boxed regions) of CLS_pld from mitochondriate protists. Amino acid positions are numbered relative to the Plasmodium knowlesi ortholog (gi: 221058144).

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Additional file 4:

Figure S3. The identified conserved motifs of CLD of eukaryotes. Two conserved regions that might function as lipase and acyltransferase motifs are boxed. Amino acid positions are numbered relative to the Phytophthora ramorum ortholog (id: Pr_95977T0).

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Additional file 5:

Figure S4. The identified conserved motifs of iPLA2 of eukaryotes. Two conserved segments among iPLA2 are indicated by lines marked on the head. Conserved Ser and Asp residues that form a catalytic dyad, and the Gly-Gly dipeptide of the oxyanion hole are indicated by asterisks.

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Additional file 6:

Figure S5. The ML phylogenetic tree of all the CLS_cap from eukaryotes and bacteria, and PGPS homologs of bacteria, which is corresponding to the Bayesian tree of Figure 2.

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Additional file 7:

Figure S6. Phylogeny of eukaryotic homologs of CLD and bacterial similar sequences. The tree was constructed by using MrBayes 3.1.2, and is illustrated using the same conventions as Figure 1. The monophyly constraint of Fungi (Fungi1+Fungi2) passed the AU test, suggesting they might be obtained through lineage-specific gene duplication.

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Additional file 8:

Figure S7. Phylogeny of iPLA2 and related bacterial similar sequences. The tree was constructed by using MrBayes 3.1.2, and is illustrated using the same conventions as Figure 1. The rejection of monophyly hypothesis of Animalia (Animalia1+Animalia2) by AU test (0.048) argues that iPLA2 beta and gamma diverged in the ancestor of Animalia though it's hard to determine the time.

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Additional file 9:

Figure S8. Phylogeny of ALCAT and AGPAT 3/4. The tree was constructed by using MrBayes 3.1.2, and is illustrated using the same conventions as Figure 1. AGPAT 3/4 were rooted as outgroup based on our preliminary analyses. The tree is illustrated using the same conventions as in Figure 1. Alternative trees constraining all Stramenopiles as monophyly were rejected, suggesting gene duplication occurred in the ancestor of Stramenopiles.

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Additional file 10:

Figure S9. Phylogeny of the TAZ and bacterial similar sequences. The tree was constructed by using MrBayes 3.1.2, and is illustrated using the same conventions as Figure 1. Hypothetical trees constraining all Archaeplastids as monophyly were rejected, suggesting gene duplication occurred in the ancestor of Archaeplstids.

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Additional file 11:

Additional file S11. Comparision between Bayesian tree and alternative topologies

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Additional file 12:

Additional file S12. The download sites of eukaryotic genomes or EST database included in the analyses

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