Prediction of the peptidomes of Tigriopus californicus and Lepeophtheirus salmonis (Copepoda, Crustacea)

Gen Comp Endocrinol. 2014 May 15;201:87-106. doi: 10.1016/j.ygcen.2014.02.015. Epub 2014 Mar 5.

Abstract

Transcriptome mining is a powerful method for crustacean peptide discovery, especially when large sequence datasets are available and an appropriate reference is extant. Recently, a 206,041-sequence transcriptome for the copepod Calanus finmarchicus was mined for peptide-encoding transcripts, with ones for 17 families/subfamilies identified. Here, the deduced Calanus pre/preprohormones were used as templates for peptide discovery in the copepods Tigriopus californicus and Lepeophtheirus salmonis; large transcriptome shotgun assembly datasets are publicly accessible for both species. Sixty-five Tigriopus and 17 Lepeophtheirus transcripts, encompassing 22 and 13 distinct peptide families/subfamilies, respectively, were identified, with the structures of 161 and 70 unique mature peptides predicted from the deduced precursors. The identified peptides included members of the allatostatin A, allatostatin C, bursicon α, bursicon β, CAPA/periviscerokinin/pyrokinin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, FLRFamide, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, and tachykinin-related peptide families, most of which possess novel structures, though isoforms from other copepods are known. Of particular note was the discovery of novel isoforms of adipokinetic hormone-corazonin-like peptide, allatotropin, corazonin, eclosion hormone and intocin, peptide families previously unidentified in copepods. In addition, Tigriopus precursors for two previously unknown peptide groups were discovered, one encoding GSEFLamides and the other DXXRLamides; precursors for the novel FXGGXamide family were identified from both Tigriopus and Lepeophtheirus. These data not only greatly expand the catalog of known copepod peptides, but also provide strong foundations for future functional studies of peptidergic signaling in members of this ecologically important crustacean subclass.

Keywords: Bioinformatics; Crustacean; Neurohormone; Neuropeptide; Transcriptome shotgun assembly.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Computational Biology*
  • Copepoda / genetics
  • Copepoda / metabolism*
  • Crustacea / genetics
  • Crustacea / metabolism*
  • Expressed Sequence Tags
  • Molecular Sequence Data
  • Peptide Fragments / analysis
  • Peptide Fragments / genetics
  • Peptide Fragments / metabolism*
  • Peptide Hormones / analysis
  • Peptide Hormones / genetics
  • Peptide Hormones / metabolism*
  • Proteome / analysis*
  • Sequence Homology, Amino Acid

Substances

  • Peptide Fragments
  • Peptide Hormones
  • Proteome