Panel Showing the Protein-Based Phylogenies of the Cytoplasmic Dynein Subunit Families

<div><p>Species names are shown with NCBI/GenBank gene/protein names. NCBI/GenBank protein-sequence accession numbers are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-st001" target="_blank">Table S1</a>. Orthologous human, mouse, and rat gene names use the revised systematized consensus nomenclature (e.g. DYNC1H1 in humans, mouse, and rat). Relationships amongst dynein sequences of different species do <i>not</i> necessarily reflect the evolutionary relationships amongst species; see [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-b208" target="_blank">208</a>] and [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-b209" target="_blank">209</a>] for further details. Named clades are indicated in the right margins. Bayesian and maximum-likelihood bootstrap values are shown as percentages (top and bottom, respectively), adjacent to branch points. Asterisks denote bootstraps below 50%. Filled circles denote bootstraps at 100%. Scale-bar represents evolutionary distance (estimated numbers of amino-acid substitutions per site).</p><p>(A) Cytoplasmic dynein heavy chain family. <i>Chlamydomonas</i> outer arm heavy chain <i>(ODA11)</i> is used as the outgroup. DNAH12frag is the partial axonemal heavy chain fragment taken from [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020001#pgen-0020001-b023" target="_blank">23</a>]. For mouse DYNC2H1, XP_35830, only partial protein sequence (336aa) was available in the GenBank database. Adding this partial sequence to our analysis resulted in spurious clustering, therefore we obtained an extended, putative sequence by using BLAST (TBLASTN) against the mouse genome (Build 32) with human and rat sequences XP_370652 and NP_075413, respectively. Incomplete mouse genomic assembly at the <i>DYNC2H1</i> locus yielded a truncated sequence 3455 amino acids in length, 85% the length of human DYNC2H1.</p><p>(B) Cytoplasmic dynein intermediate chain family. The <i>Chlamydomonas</i> IC2 <i>(ODA6)</i> is used as the outgroup.</p><p>(C) Cytoplasmic dynein light intermediate chain family. There does not appear to be a sufficiently distant homolog in <i>Chlamydomonas</i> to be used as an outgroup in this analysis, therefore ODA11 (Q39610, a heavy chain protein) was chosen as the outgroup for this tree.</p><p>(D) Cytoplasmic dynein light chain Tctex1 family. The <i>Chlamydomonas</i> LC2 light chain is used as the outgroup.</p><p>(E) Cytoplasmic dynein light chain Roadblock family. The <i>Chlamydomonas</i> outer arm dynein LC7a, is used as the outgroup.</p><p>(F) Cytoplasmic dynein light chain LC8 family. The <i>Chlamydomonas</i> Q39579 sequence is used as an outgroup. This phylogeny is poorly resolved, with low bootstrap support values and posterior clade probabilities, most likely due to there being little variation amongst the ingroup sequences. We found good support for the LC8 light chain 1 clade, and some support for the LC8 light chain 2 clade, of four vertebrate sequences. The relationships of the two sequences, C. elegans and <i>Takifugu</i> were poorly resolved, and therefore we have not included these in the LC8 light chain 2 clade.</p>