Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior
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-crown...
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| Format: | Article |
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PeerJ Inc.
2014-05-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/396.pdf |
| _version_ | 1797424413634723840 |
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| author | Christopher N. Balakrishnan Motoko Mukai Rusty A. Gonser John C. Wingfield Sarah E. London Elaina M. Tuttle David F. Clayton |
| author_facet | Christopher N. Balakrishnan Motoko Mukai Rusty A. Gonser John C. Wingfield Sarah E. London Elaina M. Tuttle David F. Clayton |
| author_sort | Christopher N. Balakrishnan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:00:54Z |
| format | Article |
| id | doaj.art-b66047a38e12429e80b10ad03c8c6498 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:00:54Z |
| publishDate | 2014-05-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-b66047a38e12429e80b10ad03c8c64982023-12-03T00:43:59ZengPeerJ Inc.PeerJ2167-83592014-05-012e39610.7717/peerj.396396Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behaviorChristopher N. Balakrishnan0Motoko Mukai1Rusty A. Gonser2John C. Wingfield3Sarah E. London4Elaina M. Tuttle5David F. Clayton6Department of Biology and Center for Biodiversity, East Carolina University, Greenville, NC, USADepartment of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USADepartment of Biology and The Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USADepartment of Neurobiology, Physiology and Behavior, University of California, Davis, CA, USADepartment of Psychology, University of Chicago, Chicago, IL, USADepartment of Biology and The Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USADivision of Biological & Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, London, UKEmberizid 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.https://peerj.com/articles/396.pdfSong learningIlluminaRNA-seqZonotrichiaSong sparrowWhite-throated sparrow |
| spellingShingle | Christopher N. Balakrishnan Motoko Mukai Rusty A. Gonser John C. Wingfield Sarah E. London Elaina M. Tuttle David F. Clayton Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior PeerJ Song learning Illumina RNA-seq Zonotrichia Song sparrow White-throated sparrow |
| title | Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior |
| title_full | Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior |
| title_fullStr | Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior |
| title_full_unstemmed | Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior |
| title_short | Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior |
| title_sort | brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior |
| topic | Song learning Illumina RNA-seq Zonotrichia Song sparrow White-throated sparrow |
| url | https://peerj.com/articles/396.pdf |
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