Digital gene expression analysis of the zebra finch genome

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Ekblom, Robert ^a,b   Balakrishnan, Christopher N ^c   Burke, Terry ^a   Slate, Jon ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UPPSALA UNIVERSITY   (Sweden)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; TRANSCRIPTOME; HISTOCOMPATIBILITY ANTIGEN;

ANIMAL TISSUE; ANTIGEN EXPRESSION; ARTICLE; BRAIN; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FINCH; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENOME; IMMUNE SYSTEM; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; SPLEEN; TISSUE SPECIFICITY; TRANSCRIPTOMICS; ANIMAL; ANTIBODY SPECIFICITY; GENETIC TRANSCRIPTION; GENETICS; IMMUNOLOGY; METABOLISM; SIGNAL TRANSDUCTION;

TAENIOPYGIA GUTTATA; VERTEBRATA;

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; FINCHES; GENE EXPRESSION PROFILING; GENOME; HISTOCOMPATIBILITY ANTIGENS; ORGAN SPECIFICITY; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 77950535845     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-219     Document Type: Article

References (60)

1. Rottscheidt R, Harr B. Extensive additivity of gene expression differentiates subspecies of the house mouse. Genetics 2007, 177(3):1553-1567. 10.1534/genetics.107.076190, 2147974, 17947435.
2. Artieri CG, Haerty W, Singh RS. Association between levels of coding sequence divergence and gene misregulation in Drosophila male hybrids. Journal of Molecular Evolution 2007, 65(6):697-704. 10.1007/s00239-007-9048-2, 18026889.
3. Ortiz-Barrientos D, Counterman BA, Noor MAF. Gene expression divergence and the origin of hybrid dysfunctions. Genetica 2007, 129(1):71-81. 10.1007/s10709-006-0034-1, 17043744.
4. Nuzhdin SV, Wayne ML, Harmon KL, McIntyre LM. Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol 2004, 21(7):1308-1317. 10.1093/molbev/msh128, 15034135.
5. Naurin S, Bensch S, Hansson B, Johansson T, Clayton DF, Albrekt A-S, Schantz TV, Hasselquist D. A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines. Molecular Ecology Resources 2008, 8(2):275-281.
6. 't Hoen PAC, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, de Menezes RX, Boer JM, van Ommen G-JB, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucl Acids Res 2008, 36(21):141.
7. Murray D, Doran P, MacMathuna P, Moss A. In silico gene expression analysis - an overview. Molecular Cancer 2007, 6:50. 10.1186/1476-4598-6-50, 1964762, 17683638.
8. Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 2007, 17(1):69-73. 10.1101/gr.5145806, 1716268, 17095711.
9. Nielsen KL, Hogh AL, Emmersen J. DeepSAGE--digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucl Acids Res 2006, 34:e133. 10.1093/nar/gkl714, 1636492, 17028099.
10. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology 2008, 17(7):1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
11. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
12. Eveland AL, McCarty DR, Koch KE. Transcript profiling by 3'-untranslated region sequencing resolves expression of gene families. Plant Physiol 2008, 146(1):32-44. 10.1104/pp.107.108597, 2230554, 18024554.
13. Torres TT, Metta M, Ottenwälder B, Schlötterer C. Gene expression profiling by massively parallel sequencing. Genome Res 2008, 18(1):172-177. 10.1101/gr.6984908, 2134766, 18032722.
14. Piertney S, Webster L. Characterising functionally important and ecologically meaningful genetic diversity using a candidate gene approach. Genetica 2010, 138(4):419-32. 10.1007/s10709-008-9322-2, 18803023.
15. Edwards SV, Hedrick PW. Evolution and ecology of MHC molecules: from genomics to sexual selection. Trends Ecol Evol 1998, 13(8):305-311.
16. Robinson J, Malik A, Parham P, Bodmer JG, Marsh SEG. IMGT/HLA database - a sequence database for the human major histocompatibility complex. Tissue Antigens 2000, 55:280-287. 10.1034/j.1399-0039.2000.550314.x, 10777106.
17. Hosomichi K, Miller MM, Goto RM, Wang YJ, Suzuki S, Kulski JK, Nishibori M, Inoko H, Hanzawa K, Shiina T. Contribution of mutation, recombination, and gene conversion to chicken Mhc-B haplotype diversity. Journal of Immunology 2008, 181(5):3393-3399.
18. Kulski JK, Shiina T, Anzai T, Kohara S, Inoko H. Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man. Immunological Reviews 2002, 190(1):95-122. 10.1034/j.1600-065X.2002.19008.x, 12493009.
19. Piertney SB, Oliver MK. The evolutionary ecology of the major histocompatibility complex. Heredity 2006, 96(1):7-21.
20. Westerdahl H. Passerine MHC: genetic variation and disease resistance in the wild. Journal of Ornithology 2007, 148:469-477.
21. Hale ML, Verduijn MH, Møller AP, Wolff K, Petrie M. Is the peacock's train an honest signal of genetic quality at the major histocompatibility complex?. Journal of Evolutionary Biology 2009, 22(6):1284-1294. 10.1111/j.1420-9101.2009.01746.x, 19453370.
22. Penn DJ, Potts WK. The evolution of mating preferences and major histocompatibility complex genes. American Naturalist 1999, 153(2):145-164.
23. Clarke B, Kirby DRS. Maintenance of histocompatibility polymorphisms. Nature 1966, 211:999-1000. 10.1038/211999a0, 6007869.
24. Ekblom R, Sæther SA, Jacobsson P, Fiske P, Sahlman T, Grahn M, Kålås JA, Höglund J. Spatial pattern of MHC class II variation in the great snipe (Gallinago media). Molecular Ecology 2007, 16(7):1439-1451. 10.1111/j.1365-294X.2007.03281.x, 17391268.
25. International Chicken Genome Sequencing Consortium Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432(7018):695-716. 10.1038/nature03154, 15592404, International Chicken Genome Sequencing Consortium.
26. Kaiser P. The avian immune genome -- a glass half-full or half-empty?. Cytogenetic and Genome Research 2007, 117(1-4):221-230. 10.1159/000103183, 17675863.
27. Ellegren H. Molecular evolutionary genomics of birds. Cytogenetic and Genome Research 2007, 117(1-4):120-130. 10.1159/000103172, 17675852.
28. Clayton DF, Balakrishnan CN, London SE. Integrating genomes, brain and behavior in the study of songbirds. Current Biology 2009, 19:R865-R873. 10.1016/j.cub.2009.07.006, 19788884.
29. Lovell PV, Clayton DF, Replogle KL, Mello CV. Birdsong transcriptomics: neurochemical specializations of the oscine song system. PLoS ONE 2008, 3(10):e3440. 10.1371/journal.pone.0003440, 2563692, 18941504.
30. London SE, Dong S, Replogle K, Clayton DF. Developmental shifts in gene expression in the auditory forebrain during the sensitive period for song learning. Developmental Neurobiology 2009, 69(7):437-450. 10.1002/dneu.20719, 19360720.
31. Dong S, Replogle KL, Hasadsri L, Imai BS, Yau PM, Rodriguez-Zas S, Southey BR, Sweedler JV, Clayton DF. Discrete molecular states in the brain accompany changing responses to a vocal signal. Proceedings of the National Academy of Sciences 2009, 106(27):11364-11369.
32. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 19015660.
33. Wilhelm BT, Landry J-R. RNA-Seq--quantitative measurement of expression through massively parallel RNA-sequencing. Methods 2009, 48(3):249-257. 10.1016/j.ymeth.2009.03.016, 19336255.
34. Wolf JBW, Bayer T, Haubold B, Schilhabel M, Rosenstiel P, Tautz D. Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology 2010, 19(s1):162-175. 10.1111/j.1365-294X.2009.04471.x, 20331778.
35. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
36. De Boever S, Vangestel C, De Backer P, Croubels S, Sys SU. Identification and validation of housekeeping genes as internal control for gene expression in an intravenous LPS inflammation model in chickens. Veterinary Immunology and Immunopathology 2008, 122(3-4):312-317. 10.1016/j.vetimm.2007.12.002, 18272235.
37. de Jonge HJM, Fehrmann RSN, de Bont ESJM, Hofstra RMW, Gerbens F, Kamps WA, de Vries EGE, Zee AGJ, te Meerman GJ, ter Elst A. Evidence based selection of housekeeping genes. PLoS ONE 2007, 2(9):e898. 10.1371/journal.pone.0000898, 1976390, 17878933.
38. Axelsson E, Hultin-Rosenberg L, Brandstrom M, Zwahlen M, Clayton DF, Ellegren H. Natural selection in avian protein-coding genes expressed in brain. Molecular Ecology 2008, 17(12):3008-3017. 10.1111/j.1365-294X.2008.03795.x, 18482257.
39. Zhang L, Li W-H. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 2004, 21(2):236-239. 10.1093/molbev/msh010, 14595094.
40. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 2005, 3(6):e170. 10.1371/journal.pbio.0030170, 1088278,1088278, 15869325.
41. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40(12):1413-1415. 10.1038/ng.259, 18978789.
42. Cutter AD, Ward S. Sexual and temporal dynamics of molecular evolution in C. elegans development. Mol Biol Evol 2005, 22(1):178-188. 10.1093/molbev/msh267, 15371532.
43. Betran E, Long M. Dntf-2r, a young drosophila retroposed gene with specific male expression under positive darwinian selection. Genetics 2003, 164(3):977-988. 1462638, 12871908.
44. Civetta A, Rajakumar SA, Brouwers B, Bacik JP. Rapid evolution and gene-specific patterns of selection for three genes of spermatogenesis in Drosophila. Mol Biol Evol 2006, 23(3):655-662. 10.1093/molbev/msj074, 16357040.
45. Good JM, Nachman MW. Rates of protein evolution are positively correlated with developmental timing of expression during mouse spermatogenesis. Mol Biol Evol 2005, 22(4):1044-1052. 10.1093/molbev/msi087, 15647515.
46. Wang ET, Kodama G, Baldi P, Moyzis RK. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci USA 2006, 103:135-140. 10.1073/pnas.0509691102, 1317879,1317879, 16371466.
47. Hedrick PW. Balancing selection and MHC. Genetica 1999, 104:207-214.
48. Corriveau RA, Huh GS, Shatz CJ. Regulation of class I MHC gene expression in the developing and mature CNS by neural activity. Neuron 1998, 21(3):505-520. 10.1016/S0896-6273(00)80562-0, 9768838.
49. Froman DP, Kirby JD, Rhoads DD. An expressed sequence tag analysis of the chicken reproductive tract transcriptome. Poult Sci 2006, 85(8):1438-1441.
50. Warren WC, Hillier LW, Marshall JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008, 453(7192):175-183. 10.1038/nature06936, 2803040, 18464734.
51. Janitz M. Next-Generation Genome Sequencing: Towards Personalized Medicine. 2008, Heidelberg: Wiley-VCH.
52. Coombs A. The sequencing shakeup. Nat Biotech 2008, 26(10):1109-1112.
53. Stapley J, Birkhead TR, Burke T, Slate J. A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution. Genetics 2008, 179(1):651-667. 10.1534/genetics.107.086264, 2390641, 18493078.
54. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24(8):1586-1591. 10.1093/molbev/msm088, 17483113.
55. Egan A, Mahurkar A, Crabtree J, Badger J, Carlton J, Silva J. IDEA: interactive display for evolutionary analyses. BMC Bioinformatics 2008, 9:524. 10.1186/1471-2105-9-524, 2655098, 19061522.
56. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 2005, 21(5):650-659. 10.1093/bioinformatics/bti042, 15388519.
57. Mank JE, Hultin-Rosenberg L, Zwahlen M, Ellegren H. Pleiotropic constraint hampers the resolution of sexual antagonism in vertebrate gene expression. The American Naturalist 2008, 171(1):35-43. 10.1086/523954, 18171149.
58. Wu X, Watson M. CORNA: testing gene lists for regulation by microRNAs. Bioinformatics 2009, 25(6):832-833. 10.1093/bioinformatics/btp059, 2654799, 19181683.
59. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
60. R Development Core Team R: a language and environment for statistical computing. 2008, Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team.