Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 7, Issue 2, 2012, Pages 110-123

  Lenz, Petra H ^a,d   Unal, Ebru ^b   Hassett, R Patrick ^c,d   Smith, Christine M ^d   Bucklin, Ann ^b   Christie, Andrew E ^a,d   Towle, David W ^d  

^a UNIVERSITY OF HAWAII   (United States)

^b UNIVERSITY OF CONNECTICUT   (United States)

^c OHIO UNIVERSITY   (United States)

^d MOUNT DESERT ISLAND BIOLOGICAL LABORATORY   (United States)

Author keywords

Calanus finmarchicus; cDNA library; Copepoda; Crustacea; Microarray

Indexed keywords

ARTICLE; CALANUS FINMARCHICUS; COPEPOD; DOWN REGULATION; ECOLOGY; FEMALE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE FUNCTION; LIPID STORAGE; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; UPREGULATION;

ANIMALIA; CALANUS FINMARCHICUS; COPEPODA; CRUSTACEA;

EID: 84862790094     PISSN: 1744117X     EISSN: 18780407     Source Type: Journal    
DOI: 10.1016/j.cbd.2011.12.001     Document Type: Article

References (79)

1. S.F. Altschul, M.S. Boguski, W. Gish, and J.C. Wootton Issues in searching molecular sequence databases Nat. Genet. 6 1994 119 129 (Pubitemid 24188591)
2. A.M. Aruda, M.F. Baumgartner, A.M. Reitzel, and A.M. Tarrant Heat shock protein expression during stress and diapause in the marine copepod Calanus finmarchicus J. Insect Physiol. 57 2011 665 675
3. G. Beaugrand, P.C. Reid, F. Ibanez, J.A. Lindley, and M. Edwards Reorganization of North Atlantic marine copepod biodiversity and climate Science 296 2002 1692 1694 (Pubitemid 34579168)
4. G. Beaugrand, K.M. Brander, J.A. Lindley, S. Souissi, and P.C. Reid Plankton effect on cod recruitment in the North Sea Nature 426 2003 661 664 (Pubitemid 38009373)
5. D. Bonnet, R.P. Harris, S. Hay, A. Ingvarsdottir, and O. Simon Histological changes of the digestive epithelium in Calanus finmarchicus: an index of diapause? Mar. Biol. 151 2007 313 326 (Pubitemid 46339642)
6. J.E. Bron, D. Frisch, E. Goetze, S.C. Johnson, C.E. Lee, and G.A. Wyngaard Observing copepods through a genomic lens Front. Zool. 8 2011 22
7. B.A. Buckley, A.Y. Gracey, and G.N. Somero The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein level analysis J. Exp. Biol. 209 2006 2660 2667
8. R.G. Campbell, J.A. Runge, and E.G. Durbin Evidence for food limitation of Calanus finmarchicus production rates on the southern flank of Georges Bank during April 1997 Deep Sea Res. Part II 48 2001 531 549 (Pubitemid 32039948)
9. R.G. Campbell, M.M. Wagner, G.J. Teegarden, C. Boudreau, and E.G. Durbin Growth and development rates of Calanus finmarchicus reared in the laboratory Mar. Ecol. Prog. Ser. 221 2001 161 183 (Pubitemid 33072749)
10. A.E. Christie, P.H. Lenz, C.M. Smith, P. Batta Lona, E. Unal, A. Bucklin, and D.W. Towle Calanus finmarchicus cDNA library: a genomic tool for studies of zooplankton physiological ecology MDIBL Bull. 48 2009 112 113
11. R.E. Cohen, and R.G. Lough Prey field of larval herring Clupea harengus on a continental shelf spawning area Mar. Ecol. Prog. Ser. 10 1983 211 222
12. J.K. Colbourne, M.E. Pfrender, D. Gilbert, W.K. Thomas, A. Tucker, T.H. Oakley, S. Tokishita, A. Aerts, G.J. Arnold, M.K. Basu, D.J. Bauer, C.E. Caceres, L. Carmel, C. Casola, J.-H. Choi, J.C. Detter, Q. Dong, S. Dusheyko, B.D. Eads, T. Frohlich, K.A. Geiler-Samerotte, D. Gerlach, P. Hatcher, S. Jogdeo, J. Krijgsveld, E.V. Kriventseva, D. Kultz, C. Laforsch, E. Lindquist, J. Lopez, J.R. Manak, J. Muller, J. Pangilinan, R.P. Patwardhan, S. Pitluck, E.J. Pritham, A. Rechtsteiner, M. Rho, I.B. Rogozin, O. Sakarya, A. Salamov, S. Schaack, H. Shapiro, Y. Shiga, C. Skalitzky, Z. Smith, A. Souvorov, W. Sung, Z. Tang, D. Tsuchiya, H. Tu, T. Vos, M. Wang, Y.I. Wolf, H. Yamagata, T. Yamada, Y. Ye, J.R. Shaw, J. Andrews, T.J. Crease, H. Tang, S.M. Lucas, H.M. Robertson, P. Bork, E.V. Koonin, E.M. Zdobnov, I.V. Grigoriev, M. Lynch, and J.L. Boore The ecoresponsive genome of Daphnia pulex Science 331 2011 555 561
13. A. Conesa, S. Götz, J.M. García-Gómez, J. Terol, M. Talón, and M. Robles Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Bioinformatics 21 2005 3674 3676 (Pubitemid 41264107)
14. T. Dale, S. Kaartverdt, B. Ellertsen, and R. Amundsen Large-scale oceanic distribution and population structure of Calanus finmarchicus, in relation to physical environment, food and predators Mar. Biol. 139 2001 561 574 (Pubitemid 32925844)
15. E.G. Durbin, A.G. Durbin, and R.C. Beardsley Springtime nutrient and chlorophyll a concentrations in the southwestern Gulf of Maine Cont. Shelf Res. 15 1995 433 450
16. E.G. Durbin, S.L. Gilman, R.G. Campbell, and A.G. Durbin Abundance, biomass, vertical migration and estimated development rate of the copepod Calanus finmarchicus in the southern Gulf of Maine during late spring Cont. Shelf Res. 15 1995 571 591
17. E.G. Durbin, P.R. Garrahan, and M.C. Casas Abundance and distribution of Calanus finmarchicus on the Georges Bank during 1995 and 1996 ICES J. Mar. Sci. 57 2000 1664 1685 (Pubitemid 32205522)
18. R. Edgar, M. Domrachev, and A.E. Lash Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res. 30 2002 207 210 (Pubitemid 34679544)
19. O. Fiksen The adaptive timing of diapause - a search for evolutionarily robust strategies in Calanus finmarchicus ICES J. Mar. Sci. 57 2000 1825 1833 (Pubitemid 32205535)
20. F. Gaardsted, M. Zhou, V. Pavlov, A. Morozov, and K.S. Tande Mesoscale distribution and advection of overwintering Calanus finmarchicus off the shelf of northern Norway Deep Sea Res. Part I 57 2010 1465 1473
21. A.P. Gasch, P.T. Spellman, C.M. Kao, O. Carmel-Hanel, M.B. Eisen, G. Storz, D. Botstein, and P.O. Brown Genomic expression programs in the response of yeast cells to environmental changes Mol. Biol. Cell 11 2000 4241 4257
22. A. Gislason, E. Gaard, H. Debes, and T. Falkenhaug Abundance, feeding and reproduction of Calanus finmarchicus in the Irminger Sea and on the northern Mid-Atlantic Ridge in June Deep Sea Res. Part II 55 2008 72 82
23. S. Götz, J.M. García-Gómez, J. Terol, S.H. Nagaraj, M.J. Nueda, M. Robles, M. Talón, J. Dopazo, and A. Conesa High-throughput functional annotation and data mining with the Blast2GO suite Nucleic Acids Res. 36 2008 3420 3435 (Pubitemid 351859009)
24. A.Y. Gracey, and A.R. Cossins Application of microarray technology in environmental and comparative physiology Annu. Rev. Physiol. 68 2003 231 259 (Pubitemid 38249154)
25. W. Hagen, and H. Auel Seasonal adaptations and the role of lipids in oceanic zooplankton Zoology 104 2001 313 328
26. B.W. Hansen, T. Marker, P. Andreassen, E. Arashkewich, F. Carlotti, P. Lindeque, K.S. Tande, and M. Wagner Differences in life-cycle traits of Calanus finmarchicus originating from 60°N and 69°N, when reared in mesocosms at 69°N Mar. Biol. 142 2003 877 893 (Pubitemid 36695705)
27. B.H. Hansen, D. Altin, S.-H. Vang, T. Nordtrug, and A.J. Olsen Effects of naphthalene on gene transcription in Calanus finmarchicus (Crustacea: Copepoda) Aquat. Toxicol. 86 2008 157 165 (Pubitemid 351162987)
28. B.H. Hansen, T. Nordtrug, D. Altin, A. Booth, K.M. Hessen, and A.J. Olsen Gene expression of GST and CYP330A1 in lipid-rich and lipid-poor female Calanus finmarchicus (Copepoda: Crustacea) exposed to dispersed oil J. Toxicol. Environ. Health A 72 2009 131 139
29. R.P. Hassett Physiological characteristics of lipid-rich "fat" and lipid-poor "thin" morphotypes of individual Calanus finmarchicus C5 copepodites in nearshore Gulf of Maine Limnol. Oceanogr. 51 2006 997 1003
30. R.P. Hassett, P. Lenz, and D. Towle Gene expression and biochemical studies of the marine copepod Calanus finmarchicus MDIBL Bull. 49 2010 115 117
31. E.J.H. Head, L.R. Harris, and R.W. Campbell Investigations on the ecology of Calanus spp. in the Labrador Sea. I. Relationship between the phytoplankton bloom and reproduction and development of Calanus finmarchicus in spring Mar. Ecol. Prog. Ser. 193 2000 53 73 (Pubitemid 30152960)
32. M.R. Heath, J. Rasmussen, Y. Ahmed, J. Allen, C.I.H. Anderson, A.S. Brierley, L. Brown, A. Bunker, K. Cook, R. Davidson, S. Fielding, W.S.C. Gurney, R. Harris, S. Hay, S. Henson, A.G. Hirst, N.P. Holliday, A. Ingvarsdottir, X. Irigoien, P. Lindeque, D.J. Mayor, D. Montagnes, C. Moffat, R. Pollard, S. Richards, R.A. Saunders, J. Sidey, G. Smerdon, D. Speirs, P. Walsham, J. Waniek, L. Webster, and D. Wilson Spatial demography of Calanus finmarchicus in the Irminger Sea Prog. Oceanogr. 76 2008 39 88 (Pubitemid 350299055)
33. P. Helaouët, and G. Beaugrand Macroecology of Calanus finmarchicus and C. helgolandicus in the North Atlantic Ocean and adjacent seas Mar. Ecol. Prog. Ser. 345 2007 147 165 (Pubitemid 47582855)
34. P. Helaouët, G. Beaugrand, and P.C. Reid Macrophysiology of Calanus finmarchicus in the North Atlantic Ocean Prog. Oceanogr. 91 2011 217 228
35. H.-J. Hirche Diapause in the marine copepod Calanus finmarchicus - a review Ophelia 44 1996 129 143 (Pubitemid 126569040)
36. H.-J. Hirche, U. Meyer, and B. Niehoff Egg production of Calanus finmarchicus: effect of temperature, food and season Mar. Biol. 127 1997 609 620 (Pubitemid 27158879)
37. T. Hulsen, J. de Vlieg, and W. Alkema BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams BMC Genomics 9 2008 488
38. X. Irigoien Some ideas about the role of lipids in the life cycle of Calanus finmarchicus J. Plankton Res. 26 2004 259 263 (Pubitemid 38370733)
39. X. Irigoien, R.N. Head, U. Klenke, B. Meyer-Harms, D.S. Harbour, B. Niehoff, H.-J. Hirche, and R.P. Harris A high frequency time series at Weathership M, Norwegian Sea, during the 1997 spring bloom: feeding of adult female Calanus finmarchicus Mar. Ecol. Prog. Ser. 172 1998 127 137 (Pubitemid 28504226)
40. C.L. Johnson, A.W. Leising, J.A. Runge, E.J.H. Head, P. Pepin, S. Plourde, and E.G. Durbin Characteristics of Calanus finmarchicus dormancy patterns in the Northwest Atlantic ICES J. Mar. Sci. 65 2008 339 350 (Pubitemid 351774737)
41. S.H. Jónasdóttir, K. Richardson, M.R. Heath, A. Ingvarsdóttir, and A. Christoffersen Spring production of Calanus finmarchicus at the Iceland-Scotland Ridge Deep Sea Res. Part I 55 2008 471 489
42. J.E. Kammenga, M.A. Herman, N.J. Ouborg, L. Johnson, and R. Breitling Microarray challenges in ecology Trends Ecol. Evol. 22 2007 273 279 (Pubitemid 46590496)
43. M. Kanehisa, and S. Goto KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28 2000 27 30 (Pubitemid 30047706)
44. M. Kanehisa, S. Goto, M. Hattori, K.F. Aoki-Kinoshita, M. Itoh, S. Kawashima, T. Katayama, M. Araki, and M. Hirakawa From genomics to chemical genomics: new developments in KEGG Nucleic Acids Res. 34 2006 D354 D357
45. M. Kanehisa, S. Goto, M. Furumichi, M. Tanabe, and M. Hirakawa KEGG for representation and analysis of molecular networks involving diseases and drugs Nucleic Acids Res. 38 2010 D355 D360
46. D.G. Kimmel, and S. Hameed Update on the relationship between the North Atlantic Oscillation and Calanus finmarchicus Mar. Ecol. Prog. Ser. 366 2008 111 117
47. T. Kiørboe, P. Munk, K. Richardson, V. Christensen, and H. Paulsen Plankton dynamics and larval herring growth, drift, and survival in a frontal area Mar. Ecol. Prog. Ser. 44 1988 205 219
48. T. Kristiansen, R.G. Lough, F.E. Werner, E.A. Broughton, and L.J. Buckley Individual-based modeling of feeding ecology and prey selection of larval cod on Georges Bank Mar. Ecol. Prog. Ser. 376 2009 227 243
49. S.J. Madsen, T.G. Nielsen, O.M. Tervo, and J. Söderkvist Importance of feeding for egg production in Calanus finmarchicus and C. glacialis during the Arctic spring Mar. Ecol. Prog. Ser. 353 2008 177 190 (Pubitemid 351262599)
50. F. Maps, S. Plourde, and B. Zakardjian Control of dormancy by lipid metabolism in Calanus finmarchicus: a population model test Mar. Ecol. Prog. Ser. 403 2010 165 180
51. F. Maps, J.A. Runge, A. Leising, A.J. Pershing, N.R. Record, S. Plourde, and J.J. Pierson Modelling the timing and duration of dormancy in populations of Calanus finmarchicus from the Northwest Atlantic shelf J. Plankton Res. 2011 10.1093/plankt/fbr088
52. S.M. Marshall, and A.P. Orr The biology of a marine copepod 1955 Oliver & Boyd Edinburgh, UK 189 pp.
53. C.J. Meise, and J.E. O'Reilly Spatial and seasonal patterns in abundance and age-composition of Calanus finmarchicus in the Gulf of Maine and on Georges Bank: 1977-1987 Deep Sea Res. Part II 43 1996 1473 1501
54. C.B. Miller, J.A. Crain, and C.A. Morgan Oil storage variability in Calanus finmarchicus ICES J. Mar. Sci. 57 2000 1786 1799 (Pubitemid 32205532)
55. B. Niehoff Effect of starvation on the reproductive potential of Calanus finmarchicus ICES J. Mar. Sci. 57 2000 1764 1772 (Pubitemid 32205529)
56. B. Niehoff The effect of food limitation on gonad development and egg production of the planktonic copepod Calanus finmarchicus J. Exp. Mar. Biol. Ecol. 307 2004 237 259 (Pubitemid 38851987)
57. J. Parkinson, A. Anthony, J. Wasmuth, R. Schmid, A. Hedley, and M. Blaxter PartiGene - constructing partial genomes Bioinformatics 20 2004 1398 1404 (Pubitemid 38931408)
58. P. Pepin, and E.J.H. Head Seasonal and depth-dependent variations in the size and lipid contents of stage 5 copepodites of Calanus finmarchicus in the waters of the Newfoundland Shelf and the Labrador Sea Deep Sea Res. Part I 56 2009 6989-1002
59. P. Pepin, C.C. Parrish, and E.J.H. Head Late autumn condition of Calanus finmarchicus in the northwestern Atlantic: evidence of size-dependent differential feeding Mar. Ecol. Prog. Ser. 423 2011 155 166
60. H. Petursdottir, S. Falk-Petersen, H. Hop, and A. Gislason Calanus finmarchicus along the northern Mid-Atlantic Ridge: variation in fatty acid and alcohol profiles and stable isotope values, δ15N and δ13C J. Plankton Res. 32 2010 1067 1077
61. S. Plourde, and J.A. Runge Reproduction of the planktonic copepod Calanus finmarchicus in the Lower St. Lawrence Estuary: relation to the cycle of phytoplankton production and evidence for a Calanus pump Mar. Ecol. Prog. Ser. 102 1993 217 227 (Pubitemid 24417334)
62. S. Plourde, P. Pepin, and E.J.H. Head Long-term seasonal and spatial patterns in mortality and survival of Calanus finmarchicus across the Atlantic Zone Monitoring Programme region, Northwest Atlantic ICES J. Mar. Sci. 66 2009 1942 1958
63. J.E. Podrabsky, and G.N. Somero Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus J. Exp. Biol. 207 2004 2237 2254 (Pubitemid 38893562)
64. J.E. Purcell, and J.J. Grover Predation and food limitation as a cause of mortality in larval herring at a spawning ground in British Columbia Mar. Ecol. Prog. Ser. 59 1990 55 61
65. G. Reygondeau, and G. Beaugrand Future climate-driven shifts in distribution of Calanus finmarchicus Glob. Chang. Biol. 17 2011 756 766
66. J.A. Runge Egg production rates of Calanus finmarchicus in the sea off Nova Scotia Arch. Hydrobiol. Beih. Ergeb. Limnol. 21 1985 33 40
67. W.J. Saumweber, and E.G. Durbin Estimating potential diapause duration in Calanus finmarchicus Deep Sea Res. Part II 53 2006 2597 2617 (Pubitemid 44854528)
68. C. Savenkoff, L. Savard, B. Morin, and D. Chabot Main prey and predators of northern shrimp (Pandalus borealis) in northern Gulf of St. Lawrence during the mid-1980s, mid-1990s and early 2000s Canadian Technical Report of Fisheries and Aquatic Sciences 2639 2006 Fisheries and Oceans Canada
69. D.C. Speirs, W.S.C. Gurney, M.R. Heath, W. Horbelt, S.N. Wood, and B.A. de Cuevas Ocean-scale modeling of the distribution, abundance, and seasonal dynamics of the copepod Calanus finmarchicus Mar. Ecol. Prog. Ser. 313 2006 173 192 (Pubitemid 43987523)
70. C.T. Taggart, S.E. Lochmann, D.A. Griffin, K.R. Thompson, and G.L. Maillet Abundance distribution of larval cod (Gadus morhua) and zooplankton in a gyre-like water mass on the Scotian Shelf Y. Watanabe, Y. Yamashita, Y. Oozeki, Survival Strategies in Early Life Stages of Marine Resources: Proceedings of an International Workshop, Yokohama, Japan, 11-14 October 1994 1996 Balkema Press Rotterdam, The Netherlands 127 145
71. A.M. Tarrant, M.F. Baumgartner, T. Verslycke, and C.L. Johnson Differential gene expression in diapausing and active Calanus finmarchicus (Copepoda) Mar. Ecol. Prog. Ser. 355 2008 193 207 (Pubitemid 351449063)
72. The Gene Ontology Consortium Gene ontology: tool for the unification of biology Nat. Genet. 25 2000 25 29
73. D.W. Towle, and C.M. Smith Gene discovery in Carcinus maenas and Homarus americanus via expressed sequence tags Integr. Comp. Biol. 46 2006 912 918 (Pubitemid 44736427)
74. V. Tusher, R. Tibshirani, and G. Chu Significance analysis of microarrays applied to transcriptional responses to ionizing radiation Proc. Natl. Acad. Sci. U. S. A. 98 2001 5116 5121 (Pubitemid 32397092)
75. M. Voznesensky, P.H. Lenz, C. Spanings-Pierrot, and D.W. Towle Genomic approaches to detecting thermal stress in Calanus finmarchicus (Copepoda: Calanoida) J. Exp. Mar. Biol. Ecol. 311 2004 37 46 (Pubitemid 39270642)
76. M. Wagner, R.G. Campbell, and E.G. Durbin Nucleic acids and growth of Calanus finmarchicus in the laboratory under different food and temperature conditions Mar. Ecol. Prog. Ser. 221 2001 185 197 (Pubitemid 33072750)
77. Y.H. Yang, S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, and T.P. Speed Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res. 30 2002 e15
78. Q. Zheng, and X.-J. Wang GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis Nucleic Acids Res. 36 2008 W358 W363
79. I. Zinke, C.S. Schütz, J.D. Katzenberer, M. Bauer, and M.J. Pankratz Nutrient control of gene expression in Drosophila: microarray analysis of starvation and sugar-dependent response EMBO J. 21 2002 6162 6173 (Pubitemid 35415333)