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

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
John C Wingfield ◽  
Sarah E London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

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, 80% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with transcript assembly N50s ranging from 2,557 to 4,072. 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.

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

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
Elaina M Tuttle ◽  
David F Clayton ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

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, 80% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with transcript assembly N50s ranging from 2,557 to 4,072. 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.

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

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
John C Wingfield ◽  
Sarah E London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

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.

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

2014 ◽  
Author(s):  
Christopher N Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A Gonser ◽  
John C Wingfield ◽  
Sarah E London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Vocal Communication ◽  
Bird Species ◽  
Model Systems ◽  
Zonotrichia Albicollis ◽  
Protein Coding ◽  
Brain Transcriptome ◽  
Successful Isolation ◽  
Primary Determinant ◽  
Zonotrichia Leucophrys Gambelii

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.

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

PeerJ ◽  
2014 ◽  
Vol 2 ◽  
pp. e396 ◽  
Author(s):  
Christopher N. Balakrishnan ◽  
Motoko Mukai ◽  
Rusty A. Gonser ◽  
John C. Wingfield ◽  
Sarah E. London ◽  
...  
Keyword(s):  
Social Behavior ◽  
Transcriptome Sequencing ◽  
Model Systems ◽  
Brain Transcriptome

scholarly journals Mouse Model Systems of Autism Spectrum Disorder: Replicability and Informatics Signature

2019 ◽  
Author(s):  
Patricia Kabitzke ◽  
Diana Morales ◽  
Dansha He ◽  
Kimberly Cox ◽  
Jane Sutphen ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Social Behavior ◽  
Mouse Model ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Model Systems ◽  
Activity Levels ◽  
Phenotypic Differences ◽  
Genetic Mouse Model ◽  
Unitary Concept

3.AbstractBackgroundPhenotyping mouse model systems of human disease has proven to be a difficult task, with frequent poor inter- and intra-laboratory replicability and translatability, particularly in behavioral domains such as social and verbal function. However, establishing robust animal model systems with strong construct validity is of fundamental importance as they are central tools for understanding disease pathophysiology and developing therapeutics. To complete our studies of mouse model systems relevant to autism spectrum disorder (ASD), we present a replication of the main findings from our two published studies comprising five genetic mouse model systems of ASD.MethodsTo assess the robustness of our previous results, we chose the two model systems that showed the greatest phenotypic differences, the Shank3/F and Cntnap2, and repeated assessments of general health, activity, and social behavior. We additionally explored all five model systems in the same framework, comparing all results obtained in this three-yearlong effort using informatics techniques to look for commonalities and differences.ResultsResults in the current study were very similar to our previously published results. The informatics signatures of the two model systems chosen for the replication showed that they were most distinguished by activity levels. Although the two model systems were opposite in this regard, those aspects of their social behavior not confounded by activity (vocalizations) were similar.ConclusionsOur results showed high intra-laboratory replicability of results, even for those with effect sizes that were not particularly large, suggesting that discrepancies in the literature may be dependent on subtle differences in testing conditions, housing enrichment, or background strains and not so much on the variability of the behavioral phenotypes. The overall informatics analysis suggests two main classes of model systems that in some aspects lie on opposite ends of the behavioral spectrum, supporting the view that autism is not a unitary concept.

scholarly journals High-throughput sequencing is revealing genetic associations with avian plumage color

The Auk ◽  
2019 ◽  
Vol 136 (4) ◽  
Author(s):  
Erik R Funk ◽  
Scott A Taylor
Keyword(s):  
High Throughput Sequencing ◽  
Large Body ◽  
Bird Species ◽  
Genetic Associations ◽  
Plumage Color ◽  
Protein Coding ◽  
Avian Evolution ◽  
Color Changes ◽  
Coding Regions ◽  
Color Differences

Abstract Avian evolution has generated an impressive array of patterns and colors in the ~10,000 bird species that exist on Earth. Recently, a number of exciting studies have utilized whole-genome sequencing to reveal new details on the genetics of avian plumage color. These findings provide compelling evidence for genes that underlie plumage variation across a wide variety of bird species (e.g., juncos, warblers, seedeaters, and estrildid finches). While much is known about large, body-wide color changes, these species exhibit discrete color differences across small plumage patches. Many genetic differences appear to be located in regulatory regions of genes rather than in protein-coding regions, suggesting gene expression is playing a large role in the control of these color patches. Taken together, these studies have the potential to broadly facilitate further research of sexual selection and evolution in these charismatic taxa.

scholarly journals The Chromosomal Polymorphism Linked to Variation in Social Behavior in the White-Throated Sparrow (Zonotrichia albicollis) Is a Complex Rearrangement and Suppressor of Recombination

Genetics ◽  
2008 ◽  
Vol 179 (3) ◽  
pp. 1455-1468 ◽  
Author(s):  
James W. Thomas ◽  
Mario Cáceres ◽  
Joshua J. Lowman ◽  
Caroline B. Morehouse ◽  
Meghan E. Short ◽  
...  
Keyword(s):  
Social Behavior ◽  
Chromosomal Polymorphism ◽  
Zonotrichia Albicollis ◽  
Complex Rearrangement

scholarly journals Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa

GigaScience ◽  
2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Miriam Payá-Milans ◽  
Laura Poza-Viejo ◽  
Patxi San Martín-Uriz ◽  
David Lara-Astiaso ◽  
Mark D Wilkinson ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Model Systems ◽  
Epigenetic Mark ◽  
Protein Coding ◽  
Brassica Crops ◽  
Genome Wide ◽  
Floral Regulatory Genes ◽  
Complex Genome

Abstract Background Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide. Findings We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3′-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci. Conclusions We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.

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