Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

BMC Bioinformatics

Volumn 8, Issue SUPPL. 7, 2007, Pages

  Pirooznia, Mehdi ^a   Gong, Ping ^b   Guan, Xin ^b   Inouye, Laura S ^c   Yang, Kuan ^a   Perkins, Edward J ^c   Deng, Youping ^a  

^a University of Southern Mississippi   (United States)

^b SpecPro Inc   (United States)

^c U S ARMY ENGINEER RESEARCH AND DEVELOPMENT CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EARTHWORM EISENIA FETIDA; ENVIRONMENTAL CONTAMINANT; EXPRESSED SEQUENCE TAGS; FUNCTIONAL ANNOTATION; PUBLICLY ACCESSIBLE; TERRESTRIAL ECOTOXICOLOGY;

COMPOSTING; DATABASE SYSTEMS; GENE EXPRESSION; YEAST;

CLONING;

COMPLEMENTARY DNA; EXPLOSIVE;

CAENORHABDITIS ELEGANS; COMPARATIVE GENOMIC HYBRIDIZATION; CONFERENCE PAPER; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EARTHWORM; EISENIA FOETIDA; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE FUNCTION; GENE MAPPING; GENETIC ANALYSIS; GENETIC DATABASE; GENOME ANALYSIS; HUMAN; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; ANIMAL; ANNELID WORM; ARTICLE; CHROMOSOME MAP; DNA SEQUENCE; DRUG EFFECT; GENETICS; METHODOLOGY; MOLECULAR GENETICS;

ANNELIDA; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EISENIA FETIDA; LUMBRICIDAE; MUS MUSCULUS; SACCHAROMYCES CEREVISIAE;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; CLONING, MOLECULAR; EXPLOSIVE AGENTS; EXPRESSED SEQUENCE TAGS; MOLECULAR SEQUENCE DATA; OLIGOCHAETA; SEQUENCE ANALYSIS, DNA;

EID: 38549115194     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S7-S7     Document Type: Conference Paper

References (33)

1. Edwards CA (Ed) Earthworm Ecology CRC Press, Boca Raton, FL Second 2004
2. Reynolds JW The status of earthworm biogeography, diversity, and taxonomy in North America revisited with glimpses into the future Earthworm Ecology CRC Press, Boca Raton, FL, USA Edwards CA 2 2004 63-74
3. Reynolds JW Status of exotic earthworm systematics and biogeography in North America Earthworm Ecology and Biogeography Lewis Publishers, CRC Press, Boca Raton, FL Hendrix PF 1995 1-28
4. Sturzenbaum SR Parkinson J Blaxter M Morgan AJ Kille P Georgiev O The earthworm expressed sequence tag project Pedobiologia 2003 47 447-451
5. Lee MS Cho SJ Tak ES Lee JA Cho HJ Park BJ Shin C Kim DK Park SC Transcriptome analysis in the midgut of the earthworm (Eisenia andrei) using expressed sequence tags Biochem Biophys Res Commun 2005 328 4 1196-204 10.1016/j.bbrc.2005.01.079 15708003
6. Deng Y Dong Y Thodima V Clem RJ Passarelli AL Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperda BMC Genomics 2006 7 264 17052344 10.1186/1471-2164-7-264
7. McCarter JP Mitreva MD Martin J Dante M Wylie T Rao U Pape D Bowers Y Theising B Murphy CV Kloek AP Chiapelli BJ Clifton SW Bird DM Waterston RH Analysis and functional classification of transcripts from the nematode Meloidogyne incognita Genome Biol 2003 4 4 R26 154577 12702207 10.1186/gb-2003-4-4-r26
8. Wang J Jemielity S Uva P Wurm Y Graff J Keller L An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta Genome Biol 2007 8 R9 1839134 17224046 10.1186/ gb-2007-8-1-r9
9. Yang GP Ross DT Kuang WW Brown PO Weigel RJ Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes Nucleic Acids Res 1999 27 6 1517-23 148347 10037815 10.1093/nar/27.6.1517
10. Ghorbel MT Sharman G Hindmarch C Becker KG Barrett T Murphy D Microarray screening of suppression subtractive hybridization-PCR cDNA libraries identifies novel RNAs regulated by dehydration in the rat supraoptic nucleus Physiol Genomics 2006 24 2 163-72 16249312
11. Soetaert A Moens LN Van der Ven K Van Leemput K Naudts B Blust R De Coen WM Molecular impact of propiconazole on Daphnia magna using a reproduction-related cDNA array Comp Biochem Physiol C Toxicol Pharmacol 2006 142 1-2 66-76 10.1016/j.cbpc.2005.10.009 16311075
12. Rim KT Park KK Sung JH Chung YH Han JH Cho KS Kim KJ Yu IJ Gene-expression profiling using suppression-subtractive hybridization and cDNA microarray in rat mononuclear cells in response to welding-fume exposure Toxicol Ind Health 2004 20 1-5 77-88 10.1191/0748233704th200oa 15807411
13. Gong P Guan X Inouye LS Pirooznia M Indest KJ Athow RS Deng Y Perkins EJ Toxicogenomics analysis provides new insights into molecular mechanisms of the sublethal toxicity of 2,4,6-trinitrotoluene in Eisenia fetida Environ Sci Technol 2007
14. Gong P Inouye LS Guan X Indest KJ Perkins EJ Interactive effects between TNT and RDX on the earthworm Eisenia fetida using a 4 k-cDNA microarray Abstract Book of SETAC North America 27th Annual Meeting, November 5-9, 2006, Montreal, PQ 364
15. Demuynck S Grumiaux F Mottier V Schikorski D Lemiere S Lepretre A Metallothionein response following cadmium exposure in the oligochaete Eisenia fetida Comp Biochem Physiol C Toxicol Pharmacol 2006 144 1 34-46 10.1016/j.cbpc.2006.05.004 16814611
16. Brulle F Mitta G Cocquerelle C Vieau D Lemiere S Lepretre A Vandenbulcke F Cloning and real-time PCR testing of 14 potential biomarkers in Eisenia fetida following cadmium exposure Environ Sci Technol 2006 40 8 2844-50 10.1021/es052299x 16683633
17. Brulle F Mitta G Leroux R Lemiere S Lepretre A Vandenbulcke F The strong induction of metallothionein gene following cadmium exposure transiently affects the expression of many genes in Eisenia fetida: A trade-off mechanism? Comp Biochem Physiol C Toxicol Pharmacol 2007 144 4 334-41 10.1016/j.cbpc.2006.10.007 17150412
18. Galay-Burgos M Spurgeon DJ Weeks JM Sturzenbaum SR Morgan AJ Kille P Developing a new method for soil pollution monitoring using molecular genetic biomarkers Biomarkers 2003 8 3-4 229-39 10.1080/ 354750031000138685 12944175
19. Diatchenko L Lau YF Campbell AP Chenchik A Moqadam F Huang B Lukyanov S Lukyanov K Gurskaya N Sverdlov ED Siebert PD Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries Proc Natl Acad Sci USA 1996 93 12 6025-6030 39182 8650213 10.1073/pnas.93.12.6025
20. Ewing B Green P Base-calling of automated sequencer traces using phred. II. Error probabilites Genome Res 1998 8 186-194 9521922
21. Nickerson DA Tobe VO Taylor SL PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing Nucleic Acids Res 1997 25 2745-2751 146817 9207020 10.1093/ nar/25.14.2745
22. Press WH Flannery BP Teukolsky SA Vetterling WT Numerical recipes in C++ The art of scientific computing Cambridge University Press, Cambridge, UK 1988
23. Giegerich R Meyer C Steffen P A discipline of dynamic programming over sequence data Sci Comput Program 2004 51 3 215-263 10.1016/ j.scico.2003.12.005
24. Chou HH Holmes MH DNA sequence quality trimming and vector removal Bioinformatics 2001 17 1093-1104 10.1093/bioinformatics/17.12.1093 11751217
25. CodonCode http://www.codoncode.com/aligner/
26. VecScreen http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html
27. Phred/Phrap/Consed; Shotgun sequence assembly http://www.phrap.org
28. Gordon D Abajian C Green P Consed: A Graphical Tool for Sequence Finishing Genome Research 1998 8 195-202 9521923
29. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000 25 25-29 10.1038/75556 10802651
30. Gene Ontology Consortium Creating the gene ontology resource: Design and implementation Genome Res 2001 11 1425-1433 311077 11483584 10.1101/ gr.180801
31. Harris MA Clark J Ireland A Lomax J Ashburner M Foulger R Eilbeck K Lewis S Marshall B Mungall C et al. The Gene Ontology (GO) database and informatics resource Nucleic Acids Res 2004 32 D258-D261 308770 14681407 10.1093/nar/gkh066
32. Ogata H Goto S Sato K Fujibuchi W Bono H Kanehisa M KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res 1999 27 29-34 148090 9847135 10.1093/nar/27.1.29
33. IUBMB Enzyme nomenclature: Recomendations of the nomenclature committee of the international union of biochemistry and molecular biology Academic Press, San Diego, CA 1992