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Data released on January 23, 2018

Supporting data for "Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning"

Colquitt, B, M; Mets, D, G; Brainard, M, S (2018): Supporting data for "Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning" GigaScience Database. http://dx.doi.org/10.5524/100398 RIS BibTeX Text

Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability, and the learning it supports, are poorly understood. To establish a platform for the molecular analysis of behavioral variability and plasticity, we have generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151x coverage and an N50 of 3.0 MB. Furthermore, we have developed an initial set of gene models using RNA-seq data from eight samples that comprise liver, muscle, cerebellum, brainstem/midbrain and forebrain tissue from juvenile and adult Bengalese finches of both sexes. We provide a draft Bengalese finch genome and gene annotation to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning. These data will directly support many avenues for the identification of genes involved in learning, including differential expression analysis, comparative genomic analysis (through comparison to existing avian genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes and gene products, enabling novel mechanistic investigations into the role of variability in learned behavior.

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Read the peer-reviewed publication(s):

Colquitt, B. M., Mets, D. G., & Brainard, M. S. (2018). Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning. GigaScience, 7(3). doi:10.1093/gigascience/giy008

Accessions (data included in GigaDB):

PROJECT: PRJNA369279

Keywords:

genome assembly systems neuroscience molecular neuroscience neural plasticity birdsong bengalese finch 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100398.jpg

Funding:

  • Funding body - National Institute of Neurological Disorders and Stroke
  • Comment - F32NS098809
  • Funding body - Howard Hughes Medical Institute

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN06283872299123Bengalese finchLonchura striata domestica Isolate:white83orange58
Alternative names:Sample name: RNA_cb_male_adult
Description:DNA extracted from the blood of adult ...
...
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SAMN08347896299123Bengalese finchLonchura striata domestica Isolate:purple31black90
Alternative names:Sample name: RNA_cb_male_adult
Description:Total RNA from adult male Bengalese fi...
...
+
SAMN08347897299123Bengalese finchLonchura striata domestica Isolate:orange47purple71
Alternative names:Sample name: RNA_cb_male_adult
Description:Total RNA from adult female Bengalese ...
...
+
SAMN08347898299123Bengalese finchLonchura striata domestica Isolate:yellow51brown12
Alternative names:Sample name: RNA_fb_male_adult
Description:Total RNA from adult male Bengalese fi...
...
+
SAMN08347899299123Bengalese finchLonchura striata domestica Isolate:white26orange56
Alternative names:Sample name: RNA_fb_female_juven...
Description:Total RNA from juvenile female Bengale...
...
+
SAMN08347900299123Bengalese finchLonchura striata domestica Isolate:white31orange73
Alternative names:Sample name: RNA_fb_male_juvenil...
Description:Total RNA from juvenile male Bengalese...
...
+
SAMN08347901299123Bengalese finchLonchura striata domestica Isolate:pink40green76
Alternative names:Sample name: RNA_liver_female_ad...
Description:Total RNA from adult female Bengalese ...
...
+
SAMN08347902299123Bengalese finchLonchura striata domestica Isolate:purple31black90
Alternative names:Sample name: RNA_mb-bs_male_adul...
Description:Total RNA from adult male Bengalese fi...
...
+
SAMN08347903299123Bengalese finchLonchura striata domestica Isolate:pink40green76
Alternative names:Sample name: RNA_muscle_female_a...
Description:Total RNA from adult female Bengalese ...
...
+
Displaying 1-9 of 9 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
annotationFASTA256.21 MB2018-01-08
annotationUNKNOWN2.92 MB2018-01-08
annotationGFF185.24 KB2018-01-08
annotationGFF34.98 MB2018-01-08
annotationFASTA52.16 MB2018-01-08
annotationGFF186.08 KB2018-01-08
BLASTUNKNOWN11.61 MB2018-01-08
Genome sequenceFASTA1.01 GB2018-01-08
mixed archiveTAR9.94 MB2018-01-08
mixed archiveTAR4.92 MB2018-01-08
Displaying 1-10 of 26 File(s).

History:

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