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

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1 Department of Biology, East Carolina University, Greenville, NC, USA
2 Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
3 Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, USA
4 Department of Biology & The Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, Indiana, USA
5 Deparment of Psychology, Institute for Mind and Body, University of Chicago, Chicago, IL, USA
6 Division of Biological & Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
DOI
10.7287/peerj.preprints.297v3
Published
Accepted
Subject Areas
Animal Behavior, Evolutionary Studies, Genomics, Neuroscience
Keywords
song learning, Illumina, RNA-seq, Zonotrichia, song sparrow, white-throated sparrow, white-crowned sparrow, zebra finch
Copyright
© 2014 Balakrishnan et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Balakrishnan CN, Mukai M, Gonser RA, Wingfield JC, London SE, Tuttle EM, Clayton DF. 2014. Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior. PeerJ PrePrints 2:e297v3

Abstract

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 a primary 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.

Author Comment

This manuscript will be submitted to PeerJ for peer review. The third version of this preprint has been edited to accommodate feedback on the original MS.