The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution

Cell & Developmental Biology, Univ, of Illinois, Urbana, IL, USA.
BMC Genomics (Impact Factor: 4.04). 02/2008; 9(1):131. DOI: 10.1186/1471-2164-9-131
Source: PubMed

ABSTRACT Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts.
We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing approximately 22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations.
Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.

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Available from: David Clayton, Aug 26, 2015
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    • ", a zebra finch Taeniopygia guttata EST microsatellite sequence DV945670 (Replogle et al. 2008) was identified with strong homology to the chicken Gallus gallus Z chromosome. We created a consensus sequence from these homologous sequences using MEGA3 (Kumar et al. 2004) and designed a primer set using PRIMER3 v0.4.0 (Rozen and Skaletsky 2000). "
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    ABSTRACT: A new primer set was developed for sex-typing birds, Z37B. This primer set was designed to amplify al-leles of small size to render it suitable for sex-typing degraded samples, including shed feathers. This marker successfully sex-typed 50 % of the species tested, including passerines, shorebirds, rails, seabirds, eagles and the brown kiwi Apteryx australis (allele size range =81–103 bp), and is therefore expected to be suitable for sex-typing a wide range of species. Z37B sex-typed non-degraded samples (blood), degraded tissue (dead unhatched embryos, dead nestlings and museum specimens) and samples of low quantity DNA (plucked feathers and buccal swabs). The small amplicon sizes in birds suggest that this marker will be of utility for sex-typing feathers, swabs and degraded samples from a wide range of avian species.
    Conservation Genetics Resources 02/2015; 7(2). DOI:10.1007/s12686-015-0429-3 · 1.14 Impact Factor
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    • "Zebra finches are songbirds that communicate using learned vocalizations (Immelmann, 1969; Miller, 1979; Clayton, 1988), and have become important model organisms for studying the neural and genomic mechanisms of social learning, memory, and sex-linked behavior (Replogle et al., 2008; Robinson et al., 2008; Clayton et al., 2009; Clayton, 2013). Both the act of singing, and the experience of hearing other birds sing, can elicit complex changes in gene expression in discrete regions of the higher forebrain (reviewed in Clayton, 2013). "
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    ABSTRACT: Natural experience can cause complex changes in gene expression in brain centers for cognition and perception, but the mechanisms that link perceptual experience and neurogenomic regulation are not understood. MicroRNAs (miRNAs or miRs) have the potential to regulate large gene expression networks, and a previous study showed that a natural perceptual stimulus (hearing the sound of birdsong in zebra finches) triggers rapid changes in expression of several miRs in the auditory forebrain. Here we evaluate the functional potential of one of these, miR-2954, which has been found so far only in birds and is encoded on the Z sex chromosome. Using fluorescence in situ hybridization and immunohistochemistry, we show that miR-2954 is present in subsets of cells in the sexually dimorphic brain regions involved in song production and perception, with notable enrichment in cell nuclei. We then probe its regulatory function by inhibiting its expression in a zebra finch cell line (G266) and measuring effects on endogenous gene expression using Illumina RNA sequencing (RNA-seq). Approximately 1000 different mRNAs change in expression by 1.5-fold or more (adjusted p < 0.01), with increases in some but not all of the targets that had been predicted by Targetscan. The population of RNAs that increase after miR-2954 inhibition is notably enriched for ones involved in the MAP Kinase (MAPK) pathway, whereas the decreasing population is dominated by genes involved in ribosomes and mitochondrial function. Since song stimulation itself triggers a decrease in miR-2954 expression followed by a delayed decrease in genes encoding ribosomal and mitochondrial functions, we suggest that miR-2954 may mediate some of the neurogenomic effects of song habituation.
    Frontiers in Neuroscience 12/2014; 8(409). DOI:10.3389/fnins.2014.00409 · 3.70 Impact Factor
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    • "This wealth of information provides an excellent support for future studies that can incorporate genomic and proteomic approaches. The recent sequencing of the chicken genome will be of great help [59] [60]. Due to the sleep characteristics of the common quail similar to those in mammals and other bird species, it may be valuable to consider this avian species as a model of sleep research. "
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    ABSTRACT: As mammals, birds exhibit two sleep phases, slow wave sleep (SWS) and REM (Rapid Eye Movement) sleep characterized by presenting different electrophysiological patterns of brain activity. During SWS a high amplitude slow wave pattern in brain activity is observed. This activity is substituted by a low amplitude fast frequency pattern during REM sleep. Common quail (Coturnix coturnix) is an animal model that has provided information related to different physiological mechanisms present in man. There are reports related to its electrophysiological brain activity, however the sleep characteristics do not have been described. The objectives of this study is describing the sleep characteristics throughout the nychthemeral cycle of the common quail and consider this bird species as an avian model to analyze the regulatory mechanisms of sleep. Experiments were carried out in implanted exemplars of Coturnix coturnix. Under general anesthesia induced by ether inhalation, stainless steel electrodes were placed to register brain activity from the anterior and posterior areas during 24 continuous hours throughout the sleep-wake cycle. Ocular and motor activities were visually monitored. Quail showed four electrophysiologically and behaviorally different states of vigilance: wakefulness (53.28%), drowsiness (14.27%), slow wave sleep (30.47%) and REM sleep (1.98%). Animals presented 202 REM sleep episodes throughout the nychthemeral cycle. Sleep distribution was polyphasic; however sleep amount was significantly greater during the period corresponding to the night. Number of nocturnal REM sleep episodes was significantly greater than that of diurnal one. The quail Coturnix coturnix shows a polyphasic distribution of sleep; however the amount of this state of vigilance is significantly greater during the nocturnal period.
    Physiology & Behavior 02/2014; 129. DOI:10.1016/j.physbeh.2014.02.041 · 3.03 Impact Factor
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