6. Presentation of Histone H3 sequence data
- The full consensus sequence of histone H3 proteins in selected organisms, and the deduced ancestral forms of histone H3 are presented as complete protein sequences.
- A tree branching structure which reflects Tree-of-Life phylogenetic speciation is shown for those species where sufficient histone H3 information is available to allow an unambiguous or highly likely H3 protein sequence to be known.
- Histone H3 protein residues are numbered from 1 to 135 in the typical H3 protein present in higher eukaryotic cells, assigning the number '0' to the translation-initiating methionine which is removed from the mature H3 protein.
- Selected and consensus H3 protein sequences are marked by the unique name used in the Histones database, typically a unique GenBank identifier.
- Identical histone sequences are shown in the same color.
- Deduced changes in the H3 protein are numbered, using standard single letter amino acid codes, to identify the residues deduced before and after the identified change. Generally, in addition a color change assists in identification of a protein sequence variation.
- Deduced gene duplication events, including associated amino acid changes, are marked by a black bar.
- Multiple distinct histone H3 proteins that co-exist in the same species are shown as parallel lines that differ in color. Co-expression of all H3 variant forms is typically assumed but often has not been confirmed experimentally.
- The H3 protein evolutionary tree is presented as a simple but large pdf files for each of the major phyla, animals, plants/green algae, and fungi. These trees are constructed using phylogenetic relationships, where available.
- Some tree branches and most deep roots are more likely based on taxonomy because even semi-solid evidence for evolutionary relationships is still missing. This limit on the histone H3 evolutionary analysis, especially for lower eukaryotic clades, is currently being ameliorated by broad evolutionary analyses of multiple genes/proteins across broad representations of fundamental clades [see references 9-13].
- The tree-like branching patterns of demonstrated (or assumed) speciation with superimposed changes in H3 proteins can be browsed within the Acrobat browser Reader. Note that files may be printed on virtual paper of as much as 12 inches by 44 inches for a single tree in order to retain full legibility.
- All aligned histone H3 protein sequences are provided as images of the tables, sorted alphabetically or as presented in the phylogenetic tree. These images are fully browser compatible: just scroll across the information.
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References
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- Thatcher TH, MacGaffey J, Bowen J, Horowitz S, Shapiro DL, Gorovsky MA. "Independent evolutionary origin of histone H3.3-like variants of animals and Tetrahymena." Nucleic Acids Res. 22, 180-186, 1994.
- Mariño-Ramírez L, Hsu B, Baxevanis A, Landsman D. "The Histone Database: a comprehensive resource for histones and histone fold-containing proteins." Proteins 62(4), 838-842, 2006.
- Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC. "The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide." Nucleic Acids Res. 34, D332-334, 2006.
- Kumar S, Tamura K, Nei M. "MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment." Briefings in Bioinformatics 5, 150-163, 2004.
- Tamura K, Dudley J, Nei M, Kumar S. "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0." Mol. Biol. Evol. 24, 1596-1599, 2007.
- Maddison DR, Schulz KS (eds). "The Tree of Life Web Project." 1996-2006. Internet address: http://tolweb.org
- Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup O, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MFJR. "The new higher level classification of eukaryotes with emphasis on the taxonomy of protists." J. Eukaryot. Microbiol. 52, 399-451, 2005.
- Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H, Lang BF. "Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes." Curr. Biol. 15, 1325-1330, 2005.
- Burki F, Pawlowski J. "Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts." Mol. Biol. Evol. 23, 1922-1930, 2006.
- Simpson AG, Inagaki Y, Roger AJ. "Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes." Mol. Biol. Evol. 23, 615-625, 2006.
- Rodriguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Lang BF. "Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans." Curr. Biol. 17, 1420-1425, 2007.
- Ruiz-Trillo I, Burger G, Holland PW, King N, Lang BF, Roger AJ, Gray MW. "The origins of multicellularity: a multi-taxon genome initiative." Trends Genet. 23, 113-118, 2007.
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