Prediction of a neuropeptidome for the eyestalk ganglia of the lobster Homarus americanus using a tissue-specific de novo assembled transcriptome.
In silico transcriptome mining is a powerful tool for crustacean peptidome prediction. Using homology-based BLAST searches and a simple bioinformatics workflow, large peptidomes have recently been predicted for a variety of crustaceans, including the lobster, Homarus americanus. Interestingly, no in silico studies have been conducted on the eyestalk ganglia (lamina ganglionaris, medulla externa, medulla interna and medulla terminalis) of the lobster, although the eyestalk is the location of a major neuroendocrine complex, i.e., the X-organ-sinus gland system. Here, an H. americanus eyestalk ganglia-specific transcriptome was produced using the de novo assembler Trinity. This transcriptome was generated from 130,973,220 Illumina reads and consists of 147,542 unique contigs. Eighty-nine neuropeptide-encoding transcripts were identified from this dataset, allowing for the deduction of 62 distinct pre/preprohormones. Two hundred sixty-two neuropeptides were predicted from this set of precursors; the peptides include members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, bursicon α, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone (CHH), CHH precursor-related peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone α2, glycoprotein hormone β5, GSEFLamide, intocin, leucokinin, molt-inhibiting hormone, myosuppressin, neuroparsin, neuropeptide F, orcokinin, orcomyotropin, pigment dispersing hormone, proctolin, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide, sulfakinin, tachykinin-related peptide and trissin families. The predicted peptides expand the H. americanus eyestalk ganglia neuropeptidome approximately 7-fold, and include 78 peptides new to the lobster. The transcriptome and predicted neuropeptidome described here provide new resources for investigating peptidergic signaling within/from the lobster eyestalk ganglia.
Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA. Electronic address: crabman@pbrc.hawaii.edu.
Andrew E
AE
Christie
Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
Vittoria
V
Roncalli
Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
Matthew C
MC
Cieslak
Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
Micah G
MG
Pascual
Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
Andy
A
Yu
Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA.
Tess J
TJ
Lameyer
Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA.
Meredith E
ME
Stanhope
Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA.
Patsy S
PS
Dickinson
D000595:Amino Acid Sequence; D000818:Animals; D060829:Arthropod Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D005123:Eye / Q000254:growth & development / Q000378:metabolism*; D005724:Ganglia / Q000254:growth & development / Q000378:metabolism*; D008121:Nephropidae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000378:metabolism; D009479:Neuropeptides / Q000032:analysis*; D020543:Proteome / Q000032:analysis; D017386:Sequence Homology, Amino Acid; D059467:Transcriptome
D060829:Arthropod Proteins; D009419:Nerve Tissue Proteins; D009479:Neuropeptides; D020543:Proteome
Crustacea; Decapoda; Neurohormone; Neuropeptide; Transcriptomics; X-organ-sinus gland system