De novo assembly of a transcriptome for Calanus finmarchicus (crustacea, copepoda) - The dominant zooplankter of the North Atlantic Ocean

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Lenz, Petra H ^a   Roncalli, Vittoria ^a   Hassett, R Patrick ^b   Wu, Le Shin ^c   Cieslak, Matthew C ^a   Hartline, Daniel K ^a   Christie, Andrew E ^a  

^a UNIVERSITY OF HAWAII   (United States)

^b OHIO UNIVERSITY   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTER; NEUROTOXIN; RNA; SAXITOXIN; TRANSCRIPTOME; TRIACYLGLYCEROL; VOLTAGE GATED SODIUM CHANNEL; MESSENGER RNA;

ADULT; ARTICLE; ATLANTIC OCEAN; BASE PAIRING; CONCENTRATION (PARAMETERS); CONTIG MAPPING; COPEPOD; CRUSTACEA; DEVELOPMENTAL STAGE; DIAPAUSE; DINOFLAGELLATE; EMBRYO; ENVIRONMENTAL EXPOSURE; FEMALE; GENE; GENE DUPLICATION; GENE LIBRARY; GENE ONTOLOGY; GENETIC TRANSCRIPTION; LIFE CYCLE; LIPOGENESIS; NAUPLIUS (LARVA); NAV1 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTOSTOMIA; RNA SPLICING; ANIMAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MALE; METABOLISM; MOLECULAR GENETICS;

ANIMALS; ATLANTIC OCEAN; COPEPODA; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE ONTOLOGY; MALE; MOLECULAR SEQUENCE ANNOTATION; RNA, MESSENGER;

EID: 84896794774     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0088589     Document Type: Article

References (54)

1. Beaugrand G, Brander KM, Lindley JA, Souissi S, Reid PC (2003) Plankton effect on cod recruitment in the North Sea. Nature 426: 661-664. (Pubitemid 38009373)
2. Helaouet P, Beaugrand G (2007) Macroecology of Calanus finmarchicus and C. helgolandicus in the North Atlantic Ocean and adjacent seas. Mar Ecol-Prog Ser 345: 147-165. (Pubitemid 47582855)
3. Maps F, Runge JA, Leising A, Pershing AJ, Record NR, et al. (2012) Modelling the timing and duration of dormancy in populations of Calanus finmarchicus from the Northwest Atlantic shelf. J Plankton Res 34: 36-54.
4. Neuheimer AB, Gentleman WC, Pepin P, Head EJH (2010) Explaining regional variability in copepod recruitment: Implications for a changing climate. Prog Oceanogr 87: 94-105.
5. Speirs DC, Guirey EJ, Gurney WSC, Heath MR (2010) A length-structured partial ecosystem model for cod in the North Sea. Fish Res 106: 474-494.
6. Utne KR, Hjollo SS, Huse G, Skogen M (2012) Estimating the consumption of Calanus finmarchicus by planktivorous fish in the Norwegian Sea using a fully coupled 3D model system. Mar Biol Res 8: 527-547.
7. Bron JE, Frisch D, Goetze E, Johnson SC, Lee CE, et al. (2011) Observing copepods through a genomic lens. Front Zool 8: 22.
8. Kiko R, Melzner F (2009) Development of an in situ sampling strategy for environmental physiology of zooplankton through transcriptional profiling. 3 International symposium on the environmenal physiology of ectotherms and plants. Tsukuba, Japan.
9. Tarrant AM, Baumgartner MF, Verslycke T, Johnson CL (2008) Differential gene expression in diapausing and active Calanus finmarchicus (Copepoda). Mar Ecol-Prog Ser 355: 193-207. (Pubitemid 351449063)
10. Lenz PH, Unal E, Hassett RP, Smith CM, Bucklin A, et al. (2012) Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray. Comp Biochem Phys D 7: 110-123.
11. Unal E, Bucklin A, Lenz PH, Towle DW (2013) Gene expression of the marine copepod Calanus finmarchicus: Responses to small-scale environmental variation in the Gulf of Maine (NW Atlantic Ocean). J Exp Mar Biol Ecol 446: 76-85.
12. Riesgo A, Andrade SCS, Sharma PP, Novo M, Perez-Porro AR, et al. (2012) Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Front Zool 9: 33.
13. Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, et al. (2011) The ecoresponsive genome of Daphnia pulex. Science 331: 555-561.
14. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652.
15. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8: 1494-1512.
16. Catterall WA (2000) From ionic currents to molecular mechanisms: The structure and function of voltage-gated sodium channels. Neuron 26: 13-25.
17. Christie AE, Roncalli V, Wu LS, Ganote CL, Doak T, et al. (2013) Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. Gen Comp Endocr 187: 117-135.
18. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
19. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676. (Pubitemid 41264107)
20. Christie AE, Fontanilla TM, Nesbit KT, Lenz PH (2013) Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome. Comp Biochem Phys D 8: 165-193.
21. Christie AE, Fontanilla TM, Roncalli V, Cieslak MC, Lenz PH (2014) Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus Gen Comp Endocr 195: 28-39.
22. McLaren IA, Sevigny JM, Corkett CJ (1988) Body sizes, development rates, and genome sizes among Calanus species. Hydrobiologia 167: 275-284.
23. Dolezel J, Bartos J, Voglmayr H, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry Pt A 51A: 127-128.
24. Jung H, Lyons RE, Dinh H, Hurwood DA, McWilliam S, et al. (2011) Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): De novo assembly, annotation and marker discovery. Plos One 6: e27938.
25. Zeng V, Villanueva KE, Ewen-Campen BS, Alwes F, Browne WE, et al. (2011) De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis. BMC Genomics 12: 581.
26. Ning J, Wang MX, Li CL, Sun S (2013) Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX. Plos One 8: e63741.
27. Sousa GL, Lenz PH, Hartline DK, Christie AE (2008) Distribution of pigment dispersing hormone- and tachykinin-related peptides in the central nervous system of the copepod crustacean Calanus finmarchicus. Gen Comp Endocr 156: 454-459.
28. Christie AE, Sousa GL, Rus S, Smith CM, Towle DW, et al. (2008) Identification of A-type allatostatins possessing -YXFGI/Vamide carboxy-carboxytermini from the nervous system of the copepod crustacean Calanus finmarchicus. Gen Comp Endocr 155: 526-533. (Pubitemid 351191923)
29. Wilson CH, Christie AE (2010) Distribution of C-type allatostatin (C-AST)-like immunoreactivity in the central nervous system of the copepod Calanus finmarchicus. Gen Comp Endocrinol 167: 252-260.
30. Hull JJ, Geib SM, Fabrick JA, Brent CS (2013) Sequencing and de novo assembly of the western tarnished plant bug (Lygus hesperus) Transcriptome. Plos One 8: e55105.
31. Mallatt JM, Garey JR, Shultz JW (2004) Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol Phylogenet Evol 31: 178-191. (Pubitemid 38403330)
32. Strausfeld NJ, Andrew DR (2011) A new view of insect-crustacean relationships I. Inferences from neural cladistics and comparative neuroanatomy. Arth Struct & Dev 40: 276-288.
33. Regier JC, Shultz JW, Kambic RE (2005) Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. P Roy Soc B-Biol Sci 272: 395-401.
34. Vrablik TL, Watts JL (2012) Emerging roles for specific fatty acids in developmental processes. Gene Dev 26: 631-637.
35. Lee RF, Hagen W, Kattner G (2006) Lipid storage in marine zooplankton. Mar Ecol Prog Ser 307: 273-306. (Pubitemid 43294016)
36. Johnson CL, Runge JA, Curtis KA, Durbin EG, Hare JA, et al. (2011) Biodiversity and ecosystem function in the Gulf of Maine: Pattern and role of zooplankton and pelagic nekton. Plos One 6: e16491.
37. Miller CB, Morgan CA, Prahl FG, Sparrow MA (1998) Storage lipids of the copepod Calanus finmarchicus from Georges Bank and the Gulf of Maine. Limnol Oceanogr 43: 488-497. (Pubitemid 28290365)
38. Turchetto-Zolet AC, Maraschin FS, de Morais GL, Cagliari A, Andrade CMB, et al. (2011) Evolutionary view of acyl-CoA diacylglycerol acyltransferase (DGAT), a key enzyme in neutral lipid biosynthesis. BMC Evol Biol 11: 263.
39. Saumweber WJ, Durbin EG (2006) Estimating potential diapause duration in Calanus finmarchicus. Deep-Sea Res Pt II 53: 2597-2617. (Pubitemid 44854528)
40. Sargent JR, Henderson RJ (1986) Lipids. In: Corner EDS, O'Hara SCM, editors. The Biological Chemistry of Marine Copepods. Oxford: Clarendon Press. 59-108.
41. Sim C, Denlinger DL (2009) Transcription profiling and regulation of fat metabolism genes in diapausing adults of the mosquito Culex pipiens. Physiol Genomics 39: 202-209.
42. Reynolds JA, Poelchau MF, Rahman Z, Armbruster PA, Denlinger DL (2012) Transcript profiling reveals mechanisms for lipid conservation during diapause in the mosquito, Aedes albopictus. J Insect Physiol 58: 966-973.
43. Reynolds JA, Hand SC (2009) Embryonic diapause highlighted by differential expression of mRNAs for ecdysteroidogenesis, transcription and lipid sparing in the cricket Allonemobius socius. J Exp Biol 212: 2074-2083.
44. Catterall WA, Goldin AL, Waxman SG (2003) International Union of Pharmacology. XXXIX. Compendium of voltage-gated ion channels: Sodium channels. Pharmacol Rev 55: 575-578. (Pubitemid 37500516)
45. Catterall WA, Goldin AL, Waxman SG (2005) International Union of Pharmacology. XLVII. Nomenclature and structure-function relationships of voltage-gated sodium channels. Pharmacol Rev 57: 397-409. (Pubitemid 43036431)
46. Goldin AL (2002) Evolution of voltage-gated Na+ channels. J Exp Biol 205: 575-584.
47. Lin WH, Wright DE, Baines RA (2009) The diversity of the paralytic voltage-gated sodium channel in Drosophila. J Neurogenet 23: S30-S30.
48. Zhang TX, Liu ZQ, Song WZ, Du YZ, Dong K (2011) Molecular characterization and functional expression of the DSC1 channel. Insect Biochem Molec 41: 451-458.
49. Barzilai MG, Reitzel AM, Kraus JEM, Gordon D, Technau U, et al. (2012) Convergent evolution of sodium ion selectivity in metazoan neuronal signaling. Cell Rep 2: 242-248.
50. Dong K (2007) Insect sodium channels and insecticide resistance. Invert Neurosci 7: 17-30.
51. Tan JG, Liu ZQ, Nomura Y, Goldin AL, Dong K (2002) Alternative splicing of an insect sodium channel gene generates pharmacologically distinct sodium channels. J Neurosci 22: 5300-5309. (Pubitemid 35386451)
52. Aruda AM, Baumgartner MF, Reitzel AM, Tarrant AM (2011) Heat shock protein expression during stress and diapause in the marine copepod Calanus finmarchicus. J Insect Physiol 57: 665-675.
53. Hansen BH, Altin D, Overjordet IB, Jager T, Nordtug T (2013) Acute exposure of water soluble fractions of marine diesel on Arctic Calanus glacialis and boreal Calanus finmarchicus: Effects on survival and biomarker response. Sci Total Environ 449: 276-284.
54. Hansen BH, Altin D, Vang SH, Nordtug T, Olsen AJ (2008) Effects of naphthalene on gene transcription in Calanus finmarchicus (Crustacea : Copepoda). Aquat Toxicol 86: 157-165. (Pubitemid 351162987)