Likely Trinity transcript errors
a: Trinity generated transcript for Eriocheir FMRFamide precursor. b: Trinity generated transcript for Scylla orcokinin precursor (Bao et al., 2015). Note that both these contigs have long internal repeats that would be highly unlikely to occur by chance and, hence, suggests that they are artefacts. Nucleotide sequences highlighted in yellow are perfect repeats. c: Alignment of several crab orcokinin precursors, providing additional arguments to suggest that the second Scylla orcokinin precursor contig is indeed an artefact.
Alignment of decapod agatoxin-like pepitdes
Note that both the sequence of the peptide as well as the presence of various transcripts of this gene are well conserved within decapods.
Sequence alignment of arthropod calcitonins
Note that the decapod calcitonins (highlighted in yellow) fit nicely in with the other arthropod calcitonins and are hence easily classified as being either A or B.
Identification of some peptide sequences found by mass spectrometry in Decapods
a: Deduced amino acid sequence of Carcinus cryptocyanin. Note that the sequence deduced from mass spectrometry data (KIFEPLRDKN) is different from the subsequence in cryptocyanin. However, this may well be an error in sequence interpretation from the mass spectrometry data as KIFEPLRENN and KIFEPLRDKN have very similar theoretical masses (1259.41 and 1259.45 respectively, versus 1259.71 found). This does not explain the KIFEPLVA peptide sequence, but given its similarity to the other peptides, it seems plausible also related to a cryptocyanin. b: Deduced amino acid sequence of Homarus thymosin containing the subsequence DLPKVDTALK found by mass spectrometry. c: Deduced amino acid sequence of Homarus histone 2A containing the subsequence AVLLPKKTEKK found by mass spectrometry. The peptide sequence KPKTEKK is perhaps PKTEKK, and if so, it would also be present in histone 2A. D: Homarus cytoplasmic type 3 actin containing the subsequence LRVAPEEHPVLL found by mass spectrometry. All protein sequences were deduced from SRAs from the respective species using Trinity. Peptides identified within these protein sequences are highlighted.