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PeerJ. 2014 May 22;2:e396. doi: 10.7717/peerj.396. eCollection 2014.

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

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Department of Biology and Center for Biodiversity, East Carolina University , Greenville, NC , USA.
Department of Food Science, College of Agriculture and Life Sciences, Cornell University , Ithaca, NY , USA ; Department of Neurobiology, Physiology and Behavior, University of California , Davis, CA , USA.
Department of Biology and The Center for Genomic Advocacy (TCGA), Indiana State University , Terre Haute, IN , USA.
Department of Neurobiology, Physiology and Behavior, University of California , Davis, CA , USA.
Department of Psychology, University of Chicago , Chicago, IL , USA.
Division of Biological & Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London , London , UK.


Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel's white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as an important determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.


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

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