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. 2011 Dec 5;6(12):e28167. doi: 10.1371/journal.pone.0028167

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Robinson et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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ClustalW alignment of (a) Dnmt1, (b) Dnmt2 and (c) MBD2/3 partial sequences. For clarity, only regions with homology to conserved motifs are presented. Sequences from a larger selection of species were used for phylogenetic analyses, but for simplicity, only a subset of these is shown here. The reported S. gregaria Dnmt1 sequence could not be aligned with the other Dnmt1 sequences presented here. Completely conserved residues are shaded black; 80–99% identical residues are dark grey; 60–79% identical residues are light grey; less than 60% identical residues are white. Alignments were constructed using MEGA4 [74] and formatted with Geneious Pro 4.8.5 [76]. Accession numbers are as follows: Acyrthosiphon pisum Dnmt1a, XP_001942687.1; A. pisum Dnmt1b, XP_001942632.1; Apis mellifera Dmnt1a, NP_001164522.1; A. mellifera Dnmt1b, XP_001122269; Bombyx mori Dnmt1, BAD67189.1; Ciona intestinalis Dnmt1, XP_002122948.1; Daphnia pulex Dnmt1, EFX80183.1; Harpegnathos saltator Dnmt1, EFN76367.1; Homo sapiens Dnmt1, NP_001124295.1; Hydra magnipapillata Dnmt1, XP_002155714.1; L. migratoria Dnmt1 type 1, FR850040; L. migratoria Dnmt1 type 2, FR850041; Pediculus humanus Dnmt1a, XP_002432160.1; P. humanus Dnmt1b, XP_002431878.1; Strongylocentrotus purpuratus Dnmt1, XP_780273.1; T. castaneum Dnmt1, XP_001814230.1; A. pisum Dnmt2, XP_001949338; A. mellifera Dnmt2, XP_393991; H. sapiens Dnmt2, 1G55_A; L. migratoria Dnmt2, FR850042; A. mellifera MBD2/3, XP_392422.2; L. migratoria Dnmt1 MBD2/3, FR850043; H. sapiens MBD2, NP_003918.1; H. sapiens MBD3, NP_003917.1. (d) Bayesian phylogenetic analysis of animal Dnmt1 sequences. In constructing the tree 339 amino acid sites were used. Posterior probabilities greater than 0.5 and the expected number of substitutions per site (scale bar) are indicated. Two distinct Pediculis humanus Dnmt1 sequences were present in GenBank. As their isoform type was not specified, they were arbitrarily named Dnmt1a and Dnmt1b. Accession numbers are listed above.