Chicken genomics resource: Sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index

Physiological Genomics

Volumn 25, Issue 3, 2006, Pages 514-524

  Carre, Wilfrid ^a   Wang, Xiaofei ^a   Porter, Tom E ^b   Nys, Yves ^c   Tang, Jianshan ^a   Bernberg, Erin ^a   Morgan, Robin ^a   Burnside, Joan ^a   Aggrey, Samuel E ^d   Simon, Jean ^c   Cogburn, Larry A ^a  

^a UNIVERSITY OF DELAWARE   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

^c STATION DE RECHERCHES AVICOLES   (France)

^d UNIVERSITY OF GEORGIA   (United States)

Author keywords

Chicken cDNA libraries; Expressed sequence tag sequence assembly; Expressed sequence tags; Gallus gallus; High throughput DNA sequencing; Nonredundant gene sets

Indexed keywords

COMPLEMENTARY DNA; CONTIG; MESSENGER RNA;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CHICKEN; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA LIBRARY; DNA MICROARRAY; EMBRYO; EXPRESSED SEQUENCE TAG; FEMALE; GENBANK; GENE CONSTRUCT; GENE SEQUENCE; GENETIC DATABASE; GENOMICS; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; UNINDEXED SEQUENCE;

ANIMALS; CHICKENS; CLUSTER ANALYSIS; CONTIG MAPPING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENOME; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 33646767077     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00207.2005     Document Type: Article

References (49)

1. Abdrakhmanov I, Lodygin D, Geroth P, Arakawa H, Law A, Plachy J, Korn B, and Buerstedde JM. A large database of chicken bursal ESTs as a resource for the analysis of vertebrate gene function. Genome Res 10: 2062-2069, 2000.
2. Ashwell CM, Czerwinski SM, Brocht SM, and McMurtry JP. Hormonal regulation of leptin expression in broiler chickens. Am J Physiol 45: 226-232, 1999.
3. Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong WT, Tickle C, Brown WRA, Wilson SA, and Hubbard SJ. A comprehensive collection of chicken cDNAs. Curr Biol 12: 1965-1969, 2002.
4. Bonaldo MF, Lennon G, and Soares MB. Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 6: 791-806, 1996.
5. Brown WRA, Hubbard SJ, and Wilson SA. The chicken as a model for large-scale analysis of vertebrate gene function. Nat Rev Genet 4: 87-98, 2003.
6. Buerstedde JM, Arakawa H, Watahiki A, Carninci PP, Hayashizaki YY, Korn B, and Plachy J. The DT40 web site: sampling and connecting the genes of a B-cell line. Nucleic Acids Res 30: 230-231, 2002.
7. Burnside J, Neiman P, Tang J, Basom R, Talbot R, Aronszajn M, Burt D, and Delrow J. Development of a cDNA array for chicken expression analysis. BMC Genomics 6: 13, 2005.
8. Burt DW. The chicken genome and the developmental biologist. Mech Dev 121: 1129-1135, 2004.
9. Chirgwin JM, Przybla AE, MacDonald RJ, and Rutter WJ. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18: 5294-5299, 1979.
10. Cogburn LA, Wang X, Carre W, Rejto L, Aggrey SE, Duclos MJ, Simon J, and Porter TE. Functional genomics in chickens: developement of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways. Comp Funct Genom 5: 253-261, 2004.
11. Cogburn LA, Wang X, Carre W, Rejto L, Porter TE, Aggrey SE, and Simon J. Systems-wide chicken DNA microarrays, gene expression profiling and discovery of functional genes. Poult Sci 82: 939-951, 2003.
12. Cui J, Sofer L, Cloud SS, and Burnside J. Patterns of gene expression in the developing chick thymus. Dev Dyn 229: 480-488, 2004.
13. Dohner JV. The Encyclopedia of Historic and Endangered Livestock and Poultry Breeds. New Haven, CT: Yale Univ. Press, 2001.
14. Ewing B and Green P. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8: 186-194, 1998.
15. Fahrenkrug SC, Smith TPL, Freking BA, Cho J, White J, Vallet J, Wise T, Rohrer G, Pertea G, Sultana R, Quackenbush J, and Keele JW. Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly. Mamm Genome 13: 475-478, 2002.
16. Friedman-Einat M, Boswell T, Horev G, Girishvarma G, Dunn IC, Talbot RT, and Sharp PJ. The chicken leptin gene: has it been cloned? Gen Comp Endocrinol 115: 354-363, 1999.
17. Glisin V, Grkvenjakov R, and Byus C. Ribonucleic acid isolation by cesium chloride centrifugation. Biochemistry 13: 2633-2637, 1974.
18. Goodridge AG and Ball EG. Lipogenesis in the pigeon: in vivo studies. Am J Physiol 213: 245-249, 1967.
19. Goodridge AG, Garay A, and Silpananta P. Regulation of lipogenesis and the total activities of lipogenic enzymes in a primary culture of hepatocytes from prenatal and early postnatal chicks. J Biol Chem 249: 1469-1475, 1974.
20. Grillasca JP, Gastaldi M, Khiri H, Dace A, Peyrol N, Reynier P, Torresani J, and Planells R. Cloning and initial characterization of human and mouse Spot 14 genes. FEBS Lett 401: 38-42, 1996.
21. Horev G, Einat P, Aharoni T, Eshdat Y, and Friedman-Einat M. Molecular cloning and properties of the chicken leptin-receptor (CLEPR) gene. Mol Cell Endocrinol 162: 95-106, 2000.
22. Huang X and Madan A. CAP3: a DNA sequence assembly program. Genome Res 9: 868-877, 1999.
23. Hubbard SJ, Grafham DV, Beattie KJ, Overton IM, McLaren SR, Croning MDR, Boardman PE, Bonfield JK, Burnside J, Davies RM, Farrell ER, Francis MD, Griffiths-Jones S, Humphray SJ, Hyland C, Scott CE, Tang H, Taylor RG, Tickle C, Brown WRA, Birney E, Rogers J, and Wilson SA. Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Res 15: 174-183, 2005.
24. Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431: 931-945, 2004.
25. International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716, 2004.
26. International Chicken Polymorphism Map Consortium. A genetic variation map for chicken with 28 million single-nucleotide polymorphisms. Nature 432: 717-722, 2004.
27. Kim H, Schmidt CJ, Decker KS, and Emara MG. A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data. Anim Genet 34: 249-254, 2003.
28. Liu HC, Cheng HH, Tirunagaru VG, Sofer L, and Burnside J. A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping. Anim Genet 32: 351-359, 2001.
29. Mao JNC, Burnside J, Postel-Vinay MC, Chambers J, Pesek J, and Cogburn LA. Ontogeny of growth hormone receptor gene expression in tissue of growth-selected strains of broiler chickens. J Endocrinol 156: 67-75, 1998.
30. Mirnics ZK, Caudell E, Gao YH, Kuwahara K, Sakaguchi N, Kurosaki T, Burnside J, Mirnics K, and Corey SJ. Microarray analysis of Lyn-deficient B cells reveals germinal center-associated nuclear protein and other genes associated with the lymphoid germinal center. J Immunol 172: 4133-4141, 2004.
31. Neiman PE, Ruddell A, Jasoni C, Loring G, Thomas SJ, Brandvold KA, Lee R, Burnside J, and Delrow J. Analysis of gene expression during myc oncogene-induced lymphomagenesis in the bursa of Fabricius. Proc Natl Acad Sci USA 98: 6378-6383, 2001.
32. Ohkubo T, Tanaka M, and Nakashima K. Structure and tissue distribution of chicken leptin receptor (cOb-R) mRNA. Biochim Biophys Acta 1491: 303-308, 2000.
33. Pennacchio LA, Olivier M, Hubacek JA, Cohen JC, Cox DR, Fruchart JC, Krauss RM, and Rubin EM. An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science 294: 169-173, 2001.
34. Pitel F, Monbrun C, Gellin J, and Vignal A. The chicken LEP (OB) gene has not been mapped. Anim Genet 31: 281, 2000.
35. Price EO. Animal Domestication and Behavior. Wallingford, UK: CABI, 2002.
36. Reich A, Jaffe N, Tong A, Lavelin I, Genina O, Pines M, Sklan D, Nussinovitch A, and Monsonego-Ornan E. Weight loading young chicks inhibits bone elongation and promotes growth plate ossification and vascularization. J Appl Physiol 98: 2381-2389, 2005.
37. Samal B, Sun Y, Stearns G, Xie C, Suggs S, and McNiece I. Cloning and characterization of the cDNA encoding a novel human pre-B-cell colony-enhancing factor. Mol Cell Biol 14: 1431-1437, 1994.
38. Seydel C. Genome research: possible new heart disease risk factor. Science 294: 33a, 2001.
39. Smith TPL, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennet GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-McKown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, and Keele JW. Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res 11: 626-630, 2001.
40. Soares MB, Bonaldo MF, Jelene P, Su L, Lawton L, and Efstratiadis A. Construction and characterization of a normalized cDNA library. Proc Natl Acad Sci USA 91: 9228-9232, 1994.
41. Sonstegard TS, Capuco A, White J, Tassell VT, Conner EE, Cho J, Sultana R, Shade L, Wray JE, Wells KD, and Quackenbush J. Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index. Mamm Genome 13: 373-379, 2002.
42. Stern CD. The chick: a great model system becomes even greater. Devel Cell 8: 9-17, 2005.
43. Taouis M, Chen JW, Daviaud C, Dupont J, Derouet M, and Simon J. Cloning the chicken leptin gene. Gene 208: 239-242, 1998.
44. Tarte-Deckert S, Chavey C, Monthouel MN, Gautier N, and van Obberghen E. The matricellular protein SPARC/osteonectin as a newly identified factor up-regulated in obesity. J Biol Chem 276: 22231-22237, 2001.
45. The FANTOM Consortium and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). The transcriptional landscape of the mammalian genome. Science 309: 1559-1563, 2005.
46. Tirunagaru VG, Sofer L, Cui J, and Burnside J. An expressed sequence tag database of T-cell-enriched activated splenocytes: sequence analysis of 5251 clones. Genomics 66: 144-151, 2000.
47. Towle HC, Kaytor EN, and Shih HM. Regulation of the expression of lipogenic enzyme genes by carbohydrate. Annu Rev Nutr 17: 405-433, 1997.
48. Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, McGrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang SP, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, de Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Schein J, Hillier LD, Mardis ER, Wilson RK, and Warren WC. A physical map of the chicken genome. Nature 432: 761-764, 2004.
49. Wang X, Carre W, Zhou H, Lamont SJ, and Cogburn LA. Duplicated Spot 14 genes in the chicken: characterization and identification of polymorphisms associated with abdominal fat traits. Gene 332: 79-88, 2004.