Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus

Abstract

The cattle tick, Rhipicephalus (Boophilus) microplus, is a pest which causes multiple health complications in cattle. The G protein-coupled receptor (GPCR) super-family presents a candidate target for developing novel tick control methods. However, GPCRs share limited sequence similarity among orthologous family members, and there is no reference genome available for R. microplus. This limits the effectiveness of alignment-dependent methods such as BLAST and Pfam for identifying GPCRs from R. microplus. However, GPCRs share a common structure consisting of seven transmembrane helices. We present an analysis of the R. microplus synganglion transcriptome using a combination of structurally-based and alignment-free methods which supplement the identification of GPCRs by sequence similarity. TMHMM predicts the number of transmembrane helices in a protein sequence. GPCRpred is a support vector machine-based method developed to predict and classify GPCRs using the dipeptide composition of a query aminoacid sequence. These two bioinformatic tools were applied to our transcriptome assembly of the cattle tick synganglion. Together, BLAST and Pfam identified 85 unique contigs as encoding partial or full length candidate cattle tick GPCRs. Collectively, TMHMM and GPCRpred identified 27 additional GPCR candidates that BLAST and Pfam missed. This demonstrates that the addition of structurally-based and alignment-free bioinformatic approaches to transcriptome annotation and analysis produces a greater collection of prospective GPCRs than an analysis based solely upon methodologies dependent upon sequence alignment and similarity.

The chemosensory appendage proteome of Amblyomma americanum (Acari: Ixodidae) reveals putative odorant‐binding and other chemoreception‐related proteins

“…Transcriptomes from the R. microplus gut (Heekin et al, 2013a), ovaries (Heekin et al, 2013b), and synganglion (Guerrero et al, 2016) were previously described. The transcriptome from the fore leg (Haller's organ) (4888 sequences) was obtained by similar methods to those described in Guerrero et al (2016).…”

“…Transcriptomes from the R. microplus gut (Heekin et al, 2013a), ovaries (Heekin et al, 2013b), and synganglion (Guerrero et al, 2016) were previously described. The transcriptome from the fore leg (Haller's organ) (4888 sequences) was obtained by similar methods to those described in Guerrero et al (2016). The R. microplus transcriptome nucleotide sequences were searched as databases against queries of protein sequences from the A. americanum proteomics analysis, using the tblastn command in BLAST+ version 2.2.31, with all parameters set at their default values.…”

Comparative morphological and transcriptomic analyses reveal novel chemosensory genes in the poultry red mite,Dermanyssus gallinaeand knockdown by RNA interference

“…Previous experiments in ticks indicated that prediction of GPCRs using transcriptome analysis might be a challenging task. As such, the transcriptome study of the bovine tick Boophilus microplus did not allow to detect the kinin receptor, a neuropeptide GPCR (Guerrero et al, 2016), which should be present (Holmes et al, 2000), underscoring the often low expression of GPCRs as a challenge for detection. Likewise, only two G proteins were identified in I. scapularis ticks and all were expressed at low to non-existent levels in legs (Josek et al, 2018).…”

Anti-tick vaccines in the omics era

“…The sialotranscriptome of A. variegatum (36), A. americanum (37)(38)(39), D. variabilis (39), I. scapularis (40,41), I. ricinus (42), D. andersoni Alarcon-Chaidez; (43) and R. appendiculatus (44) have been determined. R. microplus transcriptomes of larvae (45)(46)(47)(48)(49), engorged female gut (50), ovary (51), and synganglia (52) have been reported recently. The full-length coding sequences of numerous proteins and unique protein tick protein families have been described based in these analyses and their roles during host-parasite interaction described.…”