Figure 1.
Schematic diagram shows the nematode chemosensory gene families (NemChRs) across the analyzed taxa.
Numbers within the parenthesis in the srw column represent the actual number of the srw like sequences that clustered with the annotated srw family members from nematodes (C. elegans and P. pacificus).
Figure 2.
Phylogenetic relationships of the Rhodopsin subfamilies, the srw family from C. elegans and the srw like sequences identified from several protostome species.
The tree topology was inferred from Bayesian analysis with a gamma correction using MrBayes software. The Rhodopsin subfamilies from C. elegans included the peptide (violet), amine (light blue) and the SOG (olive green) subfamilies, among others. The major clade that clustered the novel srw like sequences with the known srw family members from nematodes (C. elegans and P. pacificus) is highlighted in red (the conserved 7TM regions of the sequences from srw clade are shown in Figure S2). Previously known srw family members from nematodes (C. elegans and P. pacificus) are marked with a star symbol. Sequences that had the highest alignment score against the 7tm_GPCR_srw domain, but failed to cluster within the srw clade are marked with black edges. Similarly, the chemosensory genes in A. californica that had the highest alignment score against the 7tm_GPCR_srw domain in our Pfam search, but clustered separately from the srw family members from nematode is highlighted in grey. We followed the same renaming for the A. californica genes as previously used [36] for easy cross verification. Abbreviations used in the figure includes, Ap (Acyrthosiphon pisum), Ag (Anopheles gambiae), Am (Apis mellifera), Ce (Caenorhabditis elegans), Df (Dictyostelium fasciculatum), Dm (Drosophila melanogaster), Dp (Daphnia pulex), Dw (Drosophila willistoni), Lg (Lottia gigantea), Ph (Pediculus humanus), Pp (Pristionchus pacificus), Sm (Schistosoma mansoni) and Nv (Nematostella vectensis). Posterior probabilities and bootstrap replicates (within parenthesis) are shown as a percentage for the major nodes.
Figure 3.
Phylogenetic relationships between the srsx, srw and the olfactory like receptors.
The phylogenetic tree includes 1) representatives of srsx family in C. elegans, 2) previously known srw family members from nematodes (C. elegans and P. pacificus), 3) srw like sequences identified in this study, 4) vertebrate olfactory genes (7tm_4), 5) olfactory like receptors in B. floridae, 6) olfactory like receptors in N. vectensis [26], 7) vertebrate olfactory sequences that had significant alignment score against the 7tm_GPCR_srsx domain (see Table S2), 8) consensus representative for each NemChR families, and 9) the sequence fragments from N. vectensis (Nv_205247) and T. adhaerens (Ta_58780) that had the highest scoring alignment against the 7tm_GPCR_Srsx domain (indicated with a star symbol). Posterior probabilities and bootstrap replicates (within parenthesis) are shown as a percentage for the major nodes.
Figure 4.
Phylogenetic trees showing closest related Rhodopsin subfamilies to the srw family.
Olfactory like genes identified in N. vectensis is used as outgroup and subsequently rooted. The Rhodopsin subfamily sequences included in the trees were obtained using srw family sequences as queries in BLASTP searches against the Rhodopsin family repertoire of C. elegans and N. vectensis. The top hits included sequences from peptide (violet), SOG (olive green), amine (dark green) subfamilies and some unclassified Rhodopsin family sequences (black) that did not have at least four of the five best hits from the same subfamily in a BLASTP search against human GPCR repertoire (see methods). The topology of trees shows that the peptide (violet) and SOG (olive green) subfamilies are placed basal to the srw clade. Posterior probabilities and the number of bootstrap replicates (within parenthesis) are shown as a percentage for the major nodes. The branches that contain srw family members from nematodes (C. elegans and P. pacificus) are indicated with a star symbol. The branches that contain sequences that are predicted to be srw in the Pfam search and yet separated from the node clustering srw family members from nematodes are indicated with hash (#) symbol. A. californica chemosensory genes that had the highest alignment score against the 7tm_GPCR_srw domain in our Pfam search is highlighted in grey box. See supplementary Figure S1 to view the phylogenetic relationships of the Rhodopsin subfamilies and the srw family in all four analyzed species (C. elegans, N. vectensis, D. melanogaster and T. adhaerens).
Figure 5.
Multiple alignments of chemosensory GPCR families and Rhodopsin like GPCR subfamilies.
Every sequence in the alignment is a consensus sequence obtained from the HMM models of the respective family using the HMMEMIT program (see materials and methods). We include consensus sequence for 1) vertebrate olfactory receptor family members from human (Hs_7tm_4), 2) srw like sequences identified in the genomes of insects, mollusk and S. mansoni (red stars), 3) Rhodopsin subfamilies from C. elegans, N. vectensis and T. adhaerens (green stars), 4) Olfactory like genes identified in N. vectensis (blue star), 5) srw like sequences identified in A. californica (yellow star), 6) 19 nematode chemosensory GPCR families from C. elegans (black stars), 7) mammalian taste receptor family (TAS2R), 8) vomeronasal receptors (V1R) and 9) the ancient Dictyostelium Cyclic AMP receptors (Dicty_CAR). The consensus sequences that are marked with a red tick symbol are obtained from Pfam HMM models downloaded from the Pfam database, while other sequences are obtained from the HMM models constructed using the multiple alignments of our sequence datasets. The red rectangular boxes indicate residues that are conserved across the srws and the Rhodopsin subgroups, whereas the black rectangular boxes indicate residues that are quite specific to the srw family.
Figure 6.
A schematic presentation of the evolution of GPCR mediated chemosensory gene families.
The eukaryotic evolutionary tree is constructed with references from the tree of life web project (http://tolweb.org/tree/phylogeny.html). Each gene family is represented with colored symbols and their presence and absence were mapped onto eukaryotic branches. A red arc represents the hypothetical origin of the gene families. The hypothetical origin of these gene families including, chordate like olfactory receptor family, vomeronasal type 1 family and taste 2 receptors were obtained from previous studies [2], [16], [18], [22], [24]. Branch lengths are not drawn to represent actual evolutionary distances.