Figure 1: Molecular Phylogenetic Analysis of Nuclear Receptors. We generated
a phylogenetic tree using the Maximum Likelihood method based on the Dayhoff matrix
based model [266] from amino acid sequences of selected conserved NRs. Sequences were
obtained from the NCBI database, aligned using Clustal W, and trimmed to include only
the extended DBD for each sequence record (this is helpful when including C. elegans
NRs, which have highly-diverged LBDs [11,185]). The tree with the highest log likelihood
(-10026.43) is shown. The small number placed at each branch indicates the percentage
of trees in which the associated taxa clustered together in 100 bootstrap replicates.
Initial tree for the heuristic search was obtained by applying Neighbor-Joining and
BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and
then selecting the topology with superior log likelihood value. The tree is drawn
to scale, with branch lengths measured in the number of substitutions per site. The
tree was rooted to the atypical (NR0) nuclear receptor knirps as an outgroup. Analysis
was conducted using MEGA7 [267]. For each class, a C. elegans (or Brugiamalayi), Drosophila,
Mus musculus, and Danio rerio ortholog was included (when present), organizing the
analysis around two ecydysozoans and two vertebrates. Additional NRs were added from
the complete genome of the echinoderm S. purpuratus, and two lophotrochozoan species.
The lophotrochozoan species included varied due to the differences in completeness
and annotation of these genomes, as well as a few possible cases of gene loss. Whenever
possible, a representative annelid and mollusk was included. Species abbreviations:
Dm Drosophila melanogaster, Ce Caenorhabditis elegans, Dr Danio rerio, Mm Mus musculus,
Bm Brugia malayi, Sp Strongylocentrotus purparatis, Ac Aplysia californica, Cg Crassostrea
gigas, Ct Capitella teleta, Hr Helobdella robusta, and Lg Lottia gigantea. This phylogenetic
analysis establishes relationships among the major conserved nuclear receptor that
is largely consistent with previously-published studies (e.g., [6]), but includes
new data from the more recently-completed invertebrate genomes.
|
|