A cDNA microarray from the telencephalon of juvenile male and female zebra finches

Wade, Juli; Peabody, Camilla; Coussens, Paul M.; Tempelman, Robert J.; Clayton, David F.; Liu, Lei; Arnold, Arthur P.; Agate, Robert J.

doi:10.1016/j.jneumeth.2004.04.007

Cited by 42 publications

(24 citation statements)

References 40 publications

(43 reference statements)

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“…Firstly, complete mRNA or genomic sequences from a wide variety of genes have been obtained from species of agricultural interest, such as turkey Meleagris gallopavo , quail Coturnix coturnix and duck Anas platyrhynchos , as well as from species used as model organisms, mainly zebra finch Taeniopygia guttata . Secondly, large-scale expressed sequence tag (EST) sequencing has been performed in zebra finch (Wade et al, 2004; see http://titan.biotec.uiuc.edu/ cgi-bin/ESTWebsite/estima_start?seqSet=songbird), and is also underway in turkey Chaves et al, 2005), quail (Mott and Ivarie, 2004), house finch Carpodacus mexicanus (Wang et al, 2006), and several others. Thirdly, the NISC Comparative Sequencing Initiative (Thomas et al, 2003) has obtained BAC clone sequence data from a few divergent bird species, including turkey, zebra finch, emu Dromaius novaehollandiae and California condor Gymnogyps californianus .…”

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confidence: 99%

Molecular evolutionary genomics of birds

Ellegren¹

2007

Cytogenet Genome Res

115

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Insight into the molecular evolution of birds has been offered by the steady accumulation of avian DNA sequence data, recently culminating in the first draft sequence of an avian genome, that of chicken. By studying avian molecular evolution we can learn about adaptations and phenotypic evolution in birds, and also gain an understanding of the similarities and differences between mammalian and avian genomes. In both these lineages, there is pronounced isochore structure with highly variable GC content. However, while mammalian isochores are decaying, they are maintained in the chicken lineage, which is consistent with a biased gene conversion model where the high and variable recombination rate of birds reinforces heterogeneity in GC. In Galliformes, GC is positively correlated with the rate of nucleotide substitution; the mean neutral mutation rate is 0.12–0.15% at each site per million years but this estimate comes with significant local variation in the rate of mutation. Comparative genomics reveals lower d_N/d_S ratios on micro- compared to macrochromosomes, possibly due to population genetic effects or a non-random distribution of genes with respect to chromosome size. A non-random genomic distribution is shown by genes with sex-biased expression, with male-biased genes over-represented and female-biased genes under-represented on the Z chromosome. A strong effect of selection is evident on the non-recombining W chromosome with high d_N/d_S ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4–5 × 10^–3 which might be seen as surprisingly high given presumed bottlenecks during domestication, but is lower than that recently observed in several natural populations of other species. Several important aspects of the molecular evolutionary process of birds remain to be understood and it can be anticipated that the upcoming genome sequence of a second bird species, the zebra finch, as well as the integration of data on gene expression, shall further advance our knowledge of avian evolution.

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confidence: 99%

Molecular evolutionary genomics of birds

Ellegren¹

2007

Cytogenet Genome Res

115

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“…There are also new genetic details to consider, specifically a surprising differential transcriptional vs. translational regulation of singing-driven ZENK that potentially serves as a mechanism for associative learning [29]. However, as zebra finch microarrays [67,68] begin to allow rapid screening for additional singing-driven genes, it will be important to identify natural environmental influences on the propensity to sing so that the function of these genes can be experimentally tested and then understood in a broader ecological context. To that end, we were aided by ethological field and laboratory studies suggesting that food availability influences singing in natural environments [51][52][53][54], which led to experimental studies of the effects of food availability on undirected singing [55,56] and the potential metabolic [57] and neurochemical systems [59][60][61][62] that convey information about food availability to the brain.…”

Section: Discussionmentioning

confidence: 99%

Singing-driven gene expression in the developing songbird brain

Johnson

Whitney

2005

Physiology & Behavior

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Neural and behavioral development arises from an integration of genetic and environmental influences, yet specifying the nature of this interaction remains a primary problem in neuroscience. Here, we review molecular and behavioral studies that focus on the role of singingdriven gene expression during neural and vocal development in the male zebra finch (Taeniopygia guttata), a songbird that learns a species-typical vocal pattern during juvenile development by imitating an adult male tutor. A primary aim of our lab has been to identify naturally-occurring environmental influences that shape the propensity to sing. This ethological approach underlies our theoretical perspective, which is to integrate the significance of singing-driven gene expression into a broader ecological context.

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“…In gene expression studies, using different fluorescent labels for different samples enables the comparison of gene expression between groups and thus differential gene expression. Microarrays have been developed to study the expression of genes involved in a wide range of functions in avian model species, such as bird song and immune reactions (Afrakhte and Schultheiss 2004;Bliss et al 2005;Burnside et al 2005;Li et al 2008;Neiman et al 2001;Smith et al 2006;Van Hemert et al 2003;Wada et al 2006;Wade et al 2004). Microarrays customised for avian model species such as Zebra Finch Taeniopygia guttata (Naurin et al 2008;Wada et al 2006) have further been used for related species (termed 'cross-species microarray analysis') (Cheviron et al 2008;Naurin et al 2012).…”

Section: Microarray Analysismentioning

confidence: 99%

Avian transcriptomics: opportunities and challenges

Jax

Kraus

2018

J Ornithol

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Recent developments in next-generation sequencing technologies have greatly facilitated the study of whole transcriptomes in model and non-model species. Studying the transcriptome and how it changes across a variety of biological conditions has had major implications for our understanding of how the genome is regulated in different contexts, and how to interpret adaptations and the phenotype of an organism. The aim of this review is to highlight the potential of these new technologies for the study of avian transcriptomics, and to summarise how transcriptomics has been applied in ornithology. A total of 81 peer-reviewed scientific articles that used transcriptomics to answer questions within a broad range of study areas in birds are used as examples throughout the review. We further provide a quick guide to highlight the most important points which need to be take into account when planning a transcriptomic study in birds, and discuss how researchers with little background in molecular biology can avoid potential pitfalls. Suggestions for further reading are supplied throughout. We also discuss possible future developments in the technology platforms used for ribonucleic acid sequencing. By summarising how these novel technologies can be used to answer questions that have long been asked by ornithologists, we hope to bridge the gap between traditional ornithology and genomics, and to stimulate more interdisciplinary research.

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A cDNA microarray from the telencephalon of juvenile male and female zebra finches

Cited by 42 publications

References 40 publications

Molecular evolutionary genomics of birds

Molecular evolutionary genomics of birds

Singing-driven gene expression in the developing songbird brain

Avian transcriptomics: opportunities and challenges

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