Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature

BMC Genomics

Volumn 9, Issue , 2008, Pages

  De Pittà, Cristiano ^a   Bertolucci, Cristiano ^b   Mazzotta, Gabriella M ^a   Bernante, Filippo ^a   Rizzo, Giorgia ^a   De Nardi, Barbara ^c   Pallavicini, Alberto ^c   Lanfranchi, Gerolamo ^a   Costa, Rodolfo ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF FERRARA   (Italy)

^c UNIVERSITY OF TRIESTE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; MICROSATELLITE DNA;

ABDOMEN; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC DATABASE; GENOME ANALYSIS; HEAD; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; RNA TRANSCRIPTION; SEQUENCE HOMOLOGY; SHRIMP; TISSUE SECTION; UNINDEXED SEQUENCE; ANIMAL; ANTIBODY SPECIFICITY; BIOLOGY; EUPHAUSIACEA; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC TRANSCRIPTION; GENETICS; HISTOLOGY; REPRODUCIBILITY; SEQUENCE ANALYSIS;

CRUSTACEA; EUPHAUSIA SUPERBA; EUPHAUSIACEA; HEXAPODA; MALACOSTRACA;

ANIMALS; COMPUTATIONAL BIOLOGY; EUPHAUSIACEA; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE LIBRARY; MICROSATELLITE REPEATS; ORGAN SPECIFICITY; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC;

EID: 41149171944     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-45     Document Type: Article

References (67)

1. Baker ADC Boden BP Brinton E A practical guide to Euphausiids of the world London: Natural history Museum Pub 1990.
2. Jarman SN Nicol S Elliot NG McMinn A 28S rDNA evolution in the Eumalacostraca and the phylogenetic position of krill Mol Phylogenet Evol 2000, 17:26-36. 10.1006/mpev.2000.0823 11020302
3. Miller DGM Hampton I Biology and ecology of the Antarctic krill Biomass Scientific Series 1989, 9:1-166.
4. Nicol S Endo Y Krill fisheries: Development, management and ecosystem implications Aquat Living Resour 1999, 12:105-120. 10.1016/ S0990-7440(99)80020-5
5. Chen YC Jaczynski J Gelation of protein recovered from whole Antarctic krill (Euphausia superba) by isoelectric solubilisation/precipitation as affected by functional additives J Agric Food Chem 2007, 55:1814-1822. 10.1021/jf0629944 17295512
6. Hewitt RP Linen Low EH The fishery on Antarctic krill: Defining an ecosystem approach to management Rev Fish Sci 2000, 8:235-298. 10.1080/ 10641260091129224
7. Taki K Hayashi T Naganobu M Characteristics of seasonal variation in diurnal vertical migration and aggregation of Antarctic krill (Euphausia superba) in the Scotia Sea, using Japanese fishery data CCAMLR Sci 2005, 12:.
8. Mauchline J The biology of mysids and euphausiids Adv Mar Biol 1980, 18:1-681.
9. Godlewska M Vertical migrations of krill (Euphausia superba, Dana) Pol Arch Hydrobiol 1996, 43:9-63.
10. Machida RJ Miya MU Yamauchi MM Nishida M Nishida S Organization of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca) Mar Biotechnol 2004, 6:238-50. 10.1007/s10126-003-0016-6 15136912
11. Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995, 270:484-487. 10.1126/science.270.5235.484 7570003
12. Liang P Pardee AB Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction Science 1992, 257:967-971. 10.1126/science.1354393 1354393
13. Adams MD Kerlavage AR Fields C Venter JC 3400 new expressed sequence tags identify diversity of transcripts in human brain Nat Genet 1993, 4:256-267. 10.1038/ng0793-256 8358434
14. Tassanakajon A Klinbunga S Paunglarp N Rimphanitchayakit V Udomkit A Jitrapakdee S Sritunyalucksana K Phongdara A Pongsomboon S Supungul P Tang S Kuphanumart K Pichyangkura R Lursinsap C Penaeus monodon gene discovery project: The generation of an EST collection and establishment of a database Gene 2006, 384:104-112. 10.1016/j.gene.2006.07.012 16945489
15. Okubo K Hori N Matoba R Nuyama T Fukushima A Kojima Y Matsubara K Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression Nat Genet 1992, 2:173-179. 10.1038/ng1192-173 1345164
16. E. superba database http://krill.cribi.unipd.it
17. Pacchioni B Trevisan S Gomirato S Toppo S Valle G Lanfranchi G Semi-multiplex PCR technique for screening of abundant transcripts during systematic sequencing of cDNA libraries Biotechniques 1996, 21:644-646. 8891215
18. Bard JBL Rhee SY Ontologies in biology: Design, applications and future challenges Nat Rev Genet 2004, 5:213-222. 10.1038/nrg1295 14970823
19. Rapp BA Wheeler DL Bioinformatics resources from the national center for biotechnology information: An integrated foundation for discovery J Am Inform Sci Technol 2005, 56:538-550. 10.1002/asi.20142
20. Toikkanen JH Miller KJ Soderlund H Jantti J Keranen S The beta subunit of the Sec61p endoplasmic reticulum translocon interacts with the exocyst complex in Saccharomyces cerevisiae J Biol Chem 2003, 278:20946-20953. 10.1074/jbc.M213111200 12665530
21. Beltramini M Colangelo N Giomi F Bubacco L Di Muro P Hellmann N Jaenicke E Decker H Quaternary structure and functional properties of Penaeus monodon hemocyanin FEBS J 2005, 272:2060-2075. 10.1111/ j.1742-4658.2005.04634.x 15819896
22. Golstein P Kroemer G Cell death by necrosis: Towards a molecular definition Trends Biochem Sci 2007, 32:37-43. 10.1016/j.tibs.2006.11.001 17141506
23. Zhang X Huang C Qin Q Antiviral properties of hemocyanin isolated from shrimp Penaeus monodon Antivir Res 2004, 61:93-99. 10.1016/ j.antiviral.2003.08.019 14670582
24. Destoumieux-Garzon D Saulnier D Garnier J Jouffrey C Bulet P Bachere E Crustacean immunity. Antifungal peptides are generated from the C terminus of shrimp hemocyanin in response to microbial challenge J Biol Chem 2001, 276:47070-47077. 10.1074/jbc.M103817200 11598107
25. Ju Z Karsi A Kocabas A Patterson A Li P Cao D Dunham R Liu Z Transcriptome analysis of channel catfish (Ictalurus punctatus): Genes and expression profile from the brain Gene 2000, 261:373-382. 10.1016/ S0378-1119(00)00491-1 11167026
26. Cao D Kocabas A Ju Z Karsi A Li P Patterson A Liu Z Transcriptome of channel catfish (Ictalurus punctatus): Initial analysis of genes and expression profiles of the head kidney Animal Genet 2001, 32:169-188. 10.1046/j.1365-2052.2001.00753.x 11531695
27. Venier P Pallavicini A De Nardi B Lanfranchi G Towards a catalogue of genes transcribed in multiple tissues of Mytilus galloprovincialis Gene 2003, 314:29-40. 10.1016/S0378-1119(03)00708-X 14527715
28. Eirin-Lopez JM Gonzalez-Tizon AM Martinez A Mendez J Birth-and-death evolution with strong purifying selection in the histone H1 multigene family and the origin of orphon H1 genes Mol Biol Evol 2004, 21:1992-2003. 10.1093/molbev/msh213 15254261
29. Hankeln T Schmidt ER The organization, localization and nucleotide sequence of the histone genes of the midge Chironomus thummi Chromosoma 1991, 101:25-31. 10.1007/BF00360683 1769271
30. Akhmanova A Miedema K Kremer H Henning W Two types of polyadenilated mRNAs are synthesized from Drosophila replication-dependent histones Eur J Biochem 1997, 244:294-300. 10.1111/j.1432-1033.1997.00294.x 9118993
31. del Gaudio R Potenza N Stefanoni P Chiusano ML Geraci G Organization and nucleotide sequence of the cluster of five histone genes in the polychaete worm Chaetopterus variopedatus: First record of a H1 histone gene in the phylum Annelida J Mol Evol 1998, 46:64-73. 10.1007/ PL00006284 9419226
32. Eirýn-Lopez JM Gonzalez-Tizon AM Martýnez A Mendez J Molecular and evolutionary analysis of mussel histone genes (Mytilus spp.): Possible evidence of an "orphon" origin for H1 histone genes J Mol Evol 2002, 55:272-283. 10.1007/s00239-002-2325-1 12187381
33. Barzotti R Pelliccia F Bucciarelli E Rocchi A Organization, nucleotide sequence, and chromosomal mapping of a tandemly repeated unit containing the four core histones genes and a 5S rRNA gene in an isopod crustacean species Genome 2000, 43:341-345. 10.1139/gen-43-2-341 10791823
34. Marino-Ramirez L Jordan IK Landsman D Multiple independent evolutionary solutions to core histone gene regulation Genome Biol 2006, 7:R122. 1794435 17184543 10.1186/gb-2006-7-12-r122
35. Bortoluzzi S Danieli GA Towards an in silico analysis of transcription patterns Trends Genet 1999, 15:118-119. 10.1016/S0168-9525(98)01682-5 10203810
36. Porter ML Cronin TW McClellan DA Crandall KA Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins Mol Biol Evol 2007, 24:253-268. 10.1093/molbev/msl152 17053049
37. Ostellari L Zane L Maccatrozzo L Bargelloni L Patarnello T Novel microsatellite loci isolated from the northern krill, Meganyctiphanes norvegica (Crustacea, Euphausiacea) Mol Ecol 2000, 9:377-8. 10.1046/ j.1365-294x.2000.00874-7.x 10736040
38. Rudd S Expressed sequence tags: Alternative or complement to whole genome sequences? Trends Plant Sci 2003, 7:321-329. 10.1016/ S1360-1385(03)00131-6
39. Jackson RB Linder CR Lynch M Purugganan M Somerville S Thayer SS Linking molecular insight and ecological research Trends Ecol Evol 2002, 17:409-414. 10.1016/S0169-5347(02)02571-5
40. Pallavicini A Del Mar Costa M Gestal C Dreos R Figueras A Venier P Novoa B High sequence variability of myticin transcripts in hemocytes of immune-stimulated mussels suggests ancient host-pathogen interactions Dev Comp Immunol 2008, 32:213-26. 10.1016/j.dci.2007.05.008 17628673
41. Parkinson J Anthony A Wasmuth J Schmid J Hedley A Blaxter M PartiGene - constructing partial genomes Bioinformatics 2004, 20:1398-1404. 10.1093/ bioinformatics/bth101 14988115
42. Parkinson J Guiliano DB Blaxter M Making sense of EST sequences by CLOBBing them BMC Bioinformatics 2002, 3:31. 137596 12398795 10.1186/ 1471-2105-3-31
43. Phrap software http://www.phrap.org
44. The National Center for Biotechnology Information ftp://ftp.ncbi.nih.gov/ blast/db
45. UniProtKB database http://www.pir.uniprot.org/database/download.shtml
46. MISA software http://pgrc.ipk-gatersleben.de/misa/
47. Rozen S Skaletsky H Primer3 on the WWW for general users and for biologist programmers Methods Mol Biol 2000, 132:365-86. 10547847
48. Schuelke M An economic method for the fluorescent labeling of PCR fragments Nature Biotechnology 2000, 18:233-234. 10.1038/72708 10657137
49. Livak KJ Schmittgen TD Analysis of relative gene expression data using Real-Time Quantitative PCR and the 2-ΔΔCt method Methods 2001, 25:402-408. 10.1006/meth.2001.1262 11846609
50. Cook CE Yue Q Akam M Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic Proc Biol Sci 2005, 272:1295-1304. 1564108 16024395 10.1098/rspb.2004.3042
51. Crease TJ The complete sequence of the mitochondrial genome of Daphnia pulex (Cladocera: Crustacea) Gene 1999, 233:89-99. 10.1016/ S0378-1119(99)00151-1 10375625
52. Umetsu K Iwabuchi N Yuasa I Saitou N Clark PF Boxshall G Osawa M Igarashi K Complete mitochondrial DNA sequence of a tadpole shrimp (Triops cancriformis) and analysis of museum samples Electrophoresis 2002, 23:4080-4084. 10.1002/elps.200290024 12481263
53. Lavrov DV Brown WM Boore JL Phylogenetic position of the Pentastomida and (pan)crustacean relationships Proc Biol Sci 2004, 271:537-544. 1691615 15129965 10.1098/rspb.2003.2631
54. Ivey JL Santos SR The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae) Gene 2007, 394:35-44. 10.1016/j.gene.2007.01.009 17317038
55. Segawa RD Aotsuka T The mitochondrial genome of the Japanese freshwater crab, Eeothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication Gene 2005, 355:28-39. 10.1016/ j.gene.2005.05.020 16039805
56. Kilpert F Podsiadlowski L The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features BMC Genomics 2006, 7:241. 1590035 16987408 10.1186/1471-2164-7-241
57. Miller AD Austin CM The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences Mol Phylogenet Evol 2006, 38:565-574. 10.1016/j.ympev.2005.10.001 16503278
58. Miller AD Murphy NP Burridge CP Austin CM Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae) Mar Biotechnol (NY) 2005, 7:339-349. 10.1007/s10126-004-4077-8 15902543
59. Yamauchi MM Miya MU Machida RJ Nishida M PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus) Mar Biotechnol (NY) 2004, 6:419-429. 10.1007/s10126-003-0036-2 15791487
60. Sun H Zhou K Song D Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements Gene 2005, 349:207-217. 10.1016/j.gene.2004.12.036 15780981
61. Miller AD Nguyen TT Burridge CP Austin CM Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (CrustaceA: Decapoda: Parastacidae): a novel gene order revealed Gene 2004, 331:65-72. 10.1016/j.gene.2004.01.022 15094192
62. Yamauchi M Miya M Nishida M Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda) Gene 2002, 295:89-96. 10.1016/S0378-1119(02)00824-7 12242015
63. Yamauchi M Miya M Nishida M Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura) Gene 2003, 311:129-135. 10.1016/S0378-1119(03)00582-1 12853147
64. Hickerson MJ Cunningham CW Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, Anomura) Mol Biol Evol 2000, 17:639-644. 10742054
65. Machida RJ Miya MU Nishida M Nishida S Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda) Mar Biotechnol (NY) 2002, 4:406-417. 10.1007/s10126-002-0033-x 14961252
66. Tjensvoll K Hodneland K Nilsen F Nylund A Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed Gene 2005, 353:218-230. 10.1016/j.gene.2005.04.033 15987668
67. Ogoh K Ohmiya Y Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions Gene 2004, 327:131-139. 10.1016/j.gene.2003.11.011 14960368