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Volumn 2014, Issue 1, 2014, Pages

Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

Author keywords

Illumina; RNA seq; Song learning; Song sparrow; White crowned sparrow; White throated sparrow; Zebra finch; Zonotrichia

Indexed keywords

TRANSCRIPTOME;

EID: 84903850933     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.396     Document Type: Article
Times cited : (27)

References (48)
  • 3
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • DOI 10.1186/gb-2010-11-10-r106.
    • Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biology 11: R106 DOI 10.1186/gb-2010-11-10-r106.
    • (2010) Genome Biology , vol.11
    • Anders, S.1    Huber, W.2
  • 4
    • 84900303930 scopus 로고    scopus 로고
    • HTSeq-a Python framework to work with high-throughput sequencing data
    • bioRxiv preprint
    • Anders S, Pyl PT, Huber W. 2014. HTSeq-a Python framework to work with high-throughput sequencing data. bioRxiv preprint.
    • (2014)
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 5
    • 84885624025 scopus 로고    scopus 로고
    • Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome
    • Article DOI 10.1098/rsob.130063.
    • Balakrishnan CN, Chapus C, Brewer MS, Clayton DF. 2013. Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome. Open Biology 3: Article 130063 DOI 10.1098/rsob.130063.
    • (2013) Open Biology , vol.3 , pp. 130063
    • Balakrishnan, C.N.1    Chapus, C.2    Brewer, M.S.3    Clayton, D.F.4
  • 6
    • 84869870731 scopus 로고    scopus 로고
    • RNA-seq transcriptome analysis of male and female zebra finch cell lines
    • DOI 10.1016/j.ygeno.2012.08.002.
    • Balakrishnan CN, Lin Y-C, London SE, Clayton DF. 2012. RNA-seq transcriptome analysis of male and female zebra finch cell lines. Genomics 100: 363-369 DOI 10.1016/j.ygeno.2012.08.002.
    • (2012) Genomics , vol.100 , pp. 363-369
    • Balakrishnan, C.N.1    Lin, Y.-C.2    London, S.E.3    Clayton, D.F.4
  • 7
    • 13844320935 scopus 로고    scopus 로고
    • Functional aspects of song learning in songbirds
    • DOI 10.1016/j.tree.2005.01.004.
    • Beecher MD, Brenowitz EA. 2005. Functional aspects of song learning in songbirds. Trends in Ecology and Evolution 20: 143-149 DOI 10.1016/j.tree.2005.01.004.
    • (2005) Trends in Ecology and Evolution , vol.20 , pp. 143-149
    • Beecher, M.D.1    Brenowitz, E.A.2
  • 9
    • 14644425886 scopus 로고    scopus 로고
    • Song learning in birds: diversity and plasticity, opportunities and challenges
    • DOI 10.1016/j.tins.2005.01.004.
    • Brenowitz EA, Beecher MD. 2005. Song learning in birds: diversity and plasticity, opportunities and challenges. Trends in Neurosciences 28: 127-132 DOI 10.1016/j.tins.2005.01.004.
    • (2005) Trends in Neurosciences , vol.28 , pp. 127-132
    • Brenowitz, E.A.1    Beecher, M.D.2
  • 10
    • 4444382330 scopus 로고    scopus 로고
    • Activation and habituation of extracellular signal-regulated kinase phosphorylation in zebra finch auditory forebrain during song presentation
    • DOI 10.1523/JNEUROSCI.1405-04.2004
    • Cheng HY, Clayton DF. 2004. Activation and habituation of extracellular signal-regulated kinase phosphorylation in zebra finch auditory forebrain during song presentation. Journal of Neuroscience 24(34): 7503-7513 DOI 10.1523/JNEUROSCI.1405-04.2004.
    • (2004) Journal of Neuroscience , vol.24 , Issue.34 , pp. 7503-7513
    • Cheng, H.Y.1    Clayton, D.F.2
  • 11
    • 80052356807 scopus 로고    scopus 로고
    • Effects of postmortem interval and preservation method on RNA isolated from field-preserved avian tissues
    • DOI 10.1525/cond.2011.100201.
    • Cheviron ZA, Carling MD, Brumfield RT. 2011. Effects of postmortem interval and preservation method on RNA isolated from field-preserved avian tissues. Condor 113: 483-489 DOI 10.1525/cond.2011.100201.
    • (2011) Condor , vol.113 , pp. 483-489
    • Cheviron, Z.A.1    Carling, M.D.2    Brumfield, R.T.3
  • 12
    • 70349291201 scopus 로고    scopus 로고
    • Integrating genomes, brain and behavior in the study of songbirds
    • DOI 10.1016/j.cub.2009.07.006.
    • Clayton DF, Balakrishnan CN, London SE. 2009. Integrating genomes, brain and behavior in the study of songbirds. Current Biology 19: R865-R873 DOI 10.1016/j.cub.2009.07.006.
    • (2009) Current Biology , vol.19
    • Clayton, D.F.1    Balakrishnan, C.N.2    London, S.E.3
  • 13
    • 0032751856 scopus 로고    scopus 로고
    • Tan and white color morphs of White-throated Sparrows differ in their non-song vocal responses to territorial intrusion
    • DOI 10.2307/1370072.
    • Collins CE, Houtman AM. 1999. Tan and white color morphs of White-throated Sparrows differ in their non-song vocal responses to territorial intrusion. Condor 101: 842-845 DOI 10.2307/1370072.
    • (1999) Condor , vol.101 , pp. 842-845
    • Collins, C.E.1    Houtman, A.M.2
  • 14
    • 0001236783 scopus 로고
    • Song development and territory establishment in Nuttals White-Crowned Sparrows
    • DOI 10.2307/1368318.
    • DeWolfe BB, Baptista LF, Petrinovich L. 1989. Song development and territory establishment in Nuttals White-Crowned Sparrows. Condor 91: 397-407 DOI 10.2307/1368318.
    • (1989) Condor , vol.91 , pp. 397-407
    • DeWolfe, B.B.1    Baptista, L.F.2    Petrinovich, L.3
  • 16
    • 77950535845 scopus 로고    scopus 로고
    • Digital gene expression analysis of the zebra finch genome
    • DOI 10.1186/1471-2164-11-219.
    • EkblomR, Balakrishnan CN, Burke T, Slate J. 2010. Digital gene expression analysis of the zebra finch genome. BMC Genomics 11: 219 DOI 10.1186/1471-2164-11-219.
    • (2010) BMC Genomics , vol.11 , pp. 219
    • Ekblom, R.1    Balakrishnan, C.N.2    Burke, T.3    Slate, J.4
  • 17
    • 84898540019 scopus 로고    scopus 로고
    • Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics
    • DOI 10.1111/1755-0998.12213
    • EkblomR, Wennekes P, Horsburgh GJ, Burke T. 2014. Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics. Molecular Ecology Resources 14(3): 636-646 DOI 10.1111/1755-0998.12213.
    • (2014) Molecular Ecology Resources , vol.14 , Issue.3 , pp. 636-646
    • Ekblom, R.1    Wennekes, P.2    Horsburgh, G.J.3    Burke, T.4
  • 18
    • 33845628839 scopus 로고    scopus 로고
    • What is immune privilege (not)?
    • DOI 10.1016/j.it.2006.11.004
    • Galea I, Bechmann I, Perry VH. 2007. What is immune privilege (not)? Trends in Immunology 28: 12-18 DOI 10.1016/j.it.2006.11.004.
    • (2007) Trends in Immunology , vol.28 , pp. 12-18
    • Galea, I.1    Bechmann, I.2    Perry, V.H.3
  • 20
    • 0032146765 scopus 로고    scopus 로고
    • A DNA test to sex most birds
    • DOI 10.1046/j.1365-294x.1998.00389.x.
    • Griffiths R, Double MC, Orr K, Dawson RJG. 1998. A DNA test to sex most birds. Molecular Ecology 7: 1071-1075 DOI 10.1046/j.1365-294x.1998.00389.x.
    • (1998) Molecular Ecology , vol.7 , pp. 1071-1075
    • Griffiths, R.1    Double, M.C.2    Orr, K.3    Dawson, R.J.G.4
  • 22
    • 84872685602 scopus 로고    scopus 로고
    • Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal
    • DOI 10.1186/1471-2164-14-52.
    • Hoffman JI, Thorne MAS, Trathan PN, Forcada J. 2013. Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics 14: 52 DOI 10.1186/1471-2164-14-52.
    • (2013) BMC Genomics , vol.14 , pp. 52
    • Hoffman, J.I.1    Thorne, M.A.S.2    Trathan, P.N.3    Forcada, J.4
  • 23
    • 79956086431 scopus 로고    scopus 로고
    • Zebra finch cell lines from naturally occurring tumors
    • DOI 10.1007/s11626-011-9392-9.
    • Itoh Y, Arnold AP. 2011. Zebra finch cell lines from naturally occurring tumors. In Vitro Cellular and Developmental Biology-Animal 47: 280-282 DOI 10.1007/s11626-011-9392-9.
    • (2011) In Vitro Cellular and Developmental Biology-Animal , vol.47 , pp. 280-282
    • Itoh, Y.1    Arnold, A.P.2
  • 24
    • 0021062739 scopus 로고
    • Differences in parental contribution among pair types in the polymorphic white-throated sparrow
    • DOI 10.1139/z83-173
    • Knapton RW, Falls JB. 1983. Differences in parental contribution among pair types in the polymorphic white-throated sparrow. Canadian Journal of Zoology 61(6): 1288-1292 DOI 10.1139/z83-173.
    • (1983) Canadian Journal of Zoology , vol.61 , Issue.6 , pp. 1288-1292
    • Knapton, R.W.1    Falls, J.B.2
  • 25
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • DOI 10.1101/gr.111120.110.
    • Lunter G, Goodson M. 2011. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research 21: 936-939 DOI 10.1101/gr.111120.110.
    • (2011) Genome Research , vol.21 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 26
    • 84871511505 scopus 로고    scopus 로고
    • Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression
    • DOI 10.1186/1471-2164-13-727.
    • Luo GZ, Hafner M, Shi Z, Brown M, Feng G-H, Tuschl T, Wang X-J, Li XC. 2012. Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression. BMC Genomics 13: 727 DOI 10.1186/1471-2164-13-727.
    • (2012) BMC Genomics , vol.13 , pp. 727
    • Luo, G.Z.1    Hafner, M.2    Shi, Z.3    Brown, M.4    Feng, G.-H.5    Tuschl, T.6    Wang, X.-J.7    Li, X.C.8
  • 27
    • 84866699534 scopus 로고    scopus 로고
    • The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis)
    • DOI 10.1371/journal.pone.0045524.
    • MacManes MD, Lacey EA. 2012. The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis). PLoS ONE 7: e45524 DOI 10.1371/journal.pone.0045524.
    • (2012) PLoS ONE , vol.7
    • MacManes, M.D.1    Lacey, E.A.2
  • 28
    • 3242691905 scopus 로고
    • Culturally transmitted patterns of vocal behavior in sparrows
    • DOI 10.1126/science.146.3650.1483.
    • Marler P, Tamura M. 1964. Culturally transmitted patterns of vocal behavior in sparrows. Science 146: 1483-1486 DOI 10.1126/science.146.3650.1483.
    • (1964) Science , vol.146 , pp. 1483-1486
    • Marler, P.1    Tamura, M.2
  • 29
    • 36448962324 scopus 로고    scopus 로고
    • A genotyping assay to determine plumage morph in the White-throated Sparrow (Zonotrichia albicollis)
    • DOI 10.1642/0004-8038(2007)124[1330: AGATDP]2.0.CO; 2
    • Michopoulos V, Maney DL, Morehouse CB, Thomas JW. 2007. A genotyping assay to determine plumage morph in the White-throated Sparrow (Zonotrichia albicollis). The Auk 124(4): 1330-1335 DOI 10.1642/0004-8038(2007)124[1330: AGATDP]2.0.CO; 2.
    • (2007) The Auk , vol.124 , Issue.4 , pp. 1330-1335
    • Michopoulos, V.1    Maney, D.L.2    Morehouse, C.B.3    Thomas, J.W.4
  • 30
    • 84879410650 scopus 로고    scopus 로고
    • The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
    • DOI 10.1111/1755-0998.12096.
    • Moghadam HK, Harrison PW, Zachar G, Szekely T, Mank JE. 2013. The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome. Molecular Ecology Resources 13: 696-705 DOI 10.1111/1755-0998.12096.
    • (2013) Molecular Ecology Resources , vol.13 , pp. 696-705
    • Moghadam, H.K.1    Harrison, P.W.2    Zachar, G.3    Szekely, T.4    Mank, J.E.5
  • 31
    • 77949523599 scopus 로고    scopus 로고
    • Seasonal differences of gene expression profiles in song sparrow (Melospiza melodia) hypothalamus in relation to territorial aggression
    • DOI 10.1371/journal.pone.0008182.
    • Mukai M, Replogle K, Drnevich J, Wang G, Wacker D, Band M, Clayton DF, Wingfield JC. 2009. Seasonal differences of gene expression profiles in song sparrow (Melospiza melodia) hypothalamus in relation to territorial aggression. PLoS ONE 4: e8182 DOI 10.1371/journal.pone.0008182.
    • (2009) PLoS ONE , vol.4
    • Mukai, M.1    Replogle, K.2    Drnevich, J.3    Wang, G.4    Wacker, D.5    Band, M.6    Clayton, D.F.7    Wingfield, J.C.8
  • 32
    • 84880005937 scopus 로고    scopus 로고
    • Assesing De Novo transcriptome assembly metrics for consistency and utility
    • DOI 10.1186/1471-2164-14-465.
    • O'Neil ST, Emrich SJ. 2013. Assesing De Novo transcriptome assembly metrics for consistency and utility. BMC Genomics 14: 465 DOI 10.1186/1471-2164-14-465.
    • (2013) BMC Genomics , vol.14 , pp. 465
    • O'Neil, S.T.1    Emrich, S.J.2
  • 34
    • 80054784996 scopus 로고    scopus 로고
    • CONDETRI-a content dependent read trimmer for illumina data
    • DOI 10.1371/journal.pone.0026314.
    • Smeds L, Kunstner A. 2011. CONDETRI-a content dependent read trimmer for illumina data. PLoS ONE 6: e26314 DOI 10.1371/journal.pone.0026314.
    • (2011) PLoS ONE , vol.6
    • Smeds, L.1    Kunstner, A.2
  • 35
    • 84864954193 scopus 로고    scopus 로고
    • Transcriptome analysis of a North American songbird, Melospiza melodia
    • DOI 10.1093/dnares/dss015.
    • Srivastava A, Winker K, Shaw TI, Jones KL, Glenn TC. 2012. Transcriptome analysis of a North American songbird, Melospiza melodia. DNA Research 19: 325-333 DOI 10.1093/dnares/dss015.
    • (2012) DNA Research , vol.19 , pp. 325-333
    • Srivastava, A.1    Winker, K.2    Shaw, T.I.3    Jones, K.L.4    Glenn, T.C.5
  • 36
    • 52049097491 scopus 로고    scopus 로고
    • The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (Zonotrichia albicollis) is a complex rearrangement and suppressor of recombination
    • DOI 10.1534/genetics.108.088229.
    • Thomas JW, Caceres M, Lowman JJ, Morehouse CB, Short ME, Baldwin EL, Maney DL, Martin CL. 2008. The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (Zonotrichia albicollis) is a complex rearrangement and suppressor of recombination. Genetics 179: 1455-1468 DOI 10.1534/genetics.108.088229.
    • (2008) Genetics , vol.179 , pp. 1455-1468
    • Thomas, J.W.1    Caceres, M.2    Lowman, J.J.3    Morehouse, C.B.4    Short, M.E.5    Baldwin, E.L.6    Maney, D.L.7    Martin, C.L.8
  • 37
    • 0038461780 scopus 로고
    • Chromosomal polymorphism in white-throated sparrow Zonotrichia albicollis (Gmelin)
    • DOI 10.1126/science.154.3756.1571.
    • Thorneycroft HB. 1966. Chromosomal polymorphism in white-throated sparrow Zonotrichia albicollis (Gmelin). Science 154: 1571-1572 DOI 10.1126/science.154.3756.1571.
    • (1966) Science , vol.154 , pp. 1571-1572
    • Thorneycroft, H.B.1
  • 38
    • 0000202198 scopus 로고
    • Cytogenetic study of white-throated sparrow, Zonotrichia albicollis (Gmelin)
    • DOI 10.2307/2407072.
    • Thorneycroft HB. 1975. Cytogenetic study of white-throated sparrow, Zonotrichia albicollis (Gmelin). Evolution 29: 611-621 DOI 10.2307/2407072.
    • (1975) Evolution , vol.29 , pp. 611-621
    • Thorneycroft, H.B.1
  • 39
    • 0038322959 scopus 로고    scopus 로고
    • Alternative reproductive strategies in the white-throated sparrow: behavioral and genetic evidence
    • DOI 10.1093/beheco/14.3.425.
    • Tuttle EM. 2003. Alternative reproductive strategies in the white-throated sparrow: behavioral and genetic evidence. Behavioral Ecology 14: 425-432 DOI 10.1093/beheco/14.3.425.
    • (2003) Behavioral Ecology , vol.14 , pp. 425-432
    • Tuttle, E.M.1
  • 40
    • 84865074382 scopus 로고    scopus 로고
    • RSeQC: quality control of RNA-seq experiments
    • DOI 10.1093/bioinformatics/bts356.
    • Wang L, Wang S, Li W. 2012. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28: 2184-2185 DOI 10.1093/bioinformatics/bts356.
    • (2012) Bioinformatics , vol.28 , pp. 2184-2185
    • Wang, L.1    Wang, S.2    Li, W.3
  • 42
    • 84872589694 scopus 로고    scopus 로고
    • Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice
    • 402-U145, DOI 10.1038/nature11816.
    • Weber JN, Peterson BK, Hoekstra HE. 2013. Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice. Nature 493: 402-U145 DOI 10.1038/nature11816.
    • (2013) Nature , vol.493
    • Weber, J.N.1    Peterson, B.K.2    Hoekstra, H.E.3
  • 43
    • 0028350915 scopus 로고
    • Regulation of territorial behavior in the sedentary song sparrow, Melospiza melodia morphna
    • DOI 10.1006/hbeh.1994.1001.
    • Wingfield JC. 1994. Regulation of territorial behavior in the sedentary song sparrow, Melospiza melodia morphna. Hormones and Behavior 28: 1-15 DOI 10.1006/hbeh.1994.1001.
    • (1994) Hormones and Behavior , vol.28 , pp. 1-15
    • Wingfield, J.C.1
  • 44
    • 0028176837 scopus 로고
    • Testosterone and territorial behavior in sedentary and migratory sparrows
    • DOI 10.1006/anbe.1994.1009.
    • Wingfield JC, Hahn TP. 1994. Testosterone and territorial behavior in sedentary and migratory sparrows. Animal Behaviour 47: 77-89 DOI 10.1006/anbe.1994.1009.
    • (1994) Animal Behaviour , vol.47 , pp. 77-89
    • Wingfield, J.C.1    Hahn, T.P.2
  • 45
    • 0036464037 scopus 로고    scopus 로고
    • Spring and autumn territoriality in song sparrows: same behavior, different mechanisms?
    • DOI 10.1093/icb/42.1.11
    • Wingfield JC, Soma KK. 2002. Spring and autumn territoriality in song sparrows: same behavior, different mechanisms? Integrative and Comparative Biology 42: 11-20 DOI 10.1093/icb/42.1.11.
    • (2002) Integrative and Comparative Biology , vol.42 , pp. 11-20
    • Wingfield, J.C.1    Soma, K.K.2
  • 47
    • 62549089305 scopus 로고    scopus 로고
    • CORNA: testing gene lists for regulation by microRNAs
    • DOI 10.1093/bioinformatics/btp059.
    • Wu X, Watson M. 2009. CORNA: testing gene lists for regulation by microRNAs. Bioinformatics 25: 832-833 DOI 10.1093/bioinformatics/btp059.
    • (2009) Bioinformatics , vol.25 , pp. 832-833
    • Wu, X.1    Watson, M.2
  • 48
    • 0033584364 scopus 로고    scopus 로고
    • Increased affiliative response to vasopressin in mice expressing the V-1a receptor from a monogamous vole
    • DOI 10.1038/23650.
    • Young LJ, Nilsen R, Waymire KG, MacGregor GR, Insel TR. 1999. Increased affiliative response to vasopressin in mice expressing the V-1a receptor from a monogamous vole. Nature 400: 766-768 DOI 10.1038/23650.
    • (1999) Nature , vol.400 , pp. 766-768
    • Young, L.J.1    Nilsen, R.2    Waymire, K.G.3    MacGregor, G.R.4    Insel, T.R.5


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