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Data released on August 23, 2017

Supporting data for "Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n=50)"

Williams, J, L; Iamartino, D; Pruitt, K, D; Sonstegard, T, S; L Smith, T, P; Low, W, Y; Biagini, T; Bomba, L; Capomaccio, S; Castiglioni, B; Coletta, A; Corrado, F; Ferre, F; Iannuzzi, L; Lawley, C; Macciotta, N; McClure, M; Mancini, G; Matassino, D; Mazza, R; Milanesi, M; Moioli, B; Morandi, N; Ramunno, L; Peretti, V; Pilla, F; Ramelli, P; Schroeder, S; Strozzi, F; Thibaud-Nissen, F; Zicarelli, L; Ajmone-Marsan, P; Valentini, A; Chillemi, G; Zimin, A (2017): Supporting data for "Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n=50)" GigaScience Database. http://dx.doi.org/10.5524/100333 RIS BibTeX Text

Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well annotated, reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are two species of domestic water buffalo, the river (2n=50) and the swamp (2n=48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler. The assembled sequence is 2.83 Gb, consisting of 366,983 scaffolds with a scaffold N50 of 1.41 Mb and contig N50 of 21,398 bp. Annotation of the genome was supported by transcriptome data from 30 tissues, and identified 21,711 predicted protein coding genes. Searches for complete mammalian BUSCO gene groups found 98.6% of curated single copy orthologs present among predicted genes, which suggests a high level of completeness of the genome. The annotated sequence is available from NCBI at accession GCA_000471725.1.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJEB4351
GENBANK: GCA_000471725.1
BioProject: PRJNA207334

Keywords:

Water buffalo Genome assembly Transcriptome Annotation 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100333.jpg

Funding:

  • Funding body - U.S. Department of Agriculture
  • Award ID - 5438-31000-073-00D
  • Awardee - TPL Smith
  • Funding body - National Institutes of Health
  • Comment - Intramural Research Program
  • Awardee - KD Pruitt

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
tongue89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
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rumen89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
abomasum89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
small_intestine89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
large_intestine89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
obex89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
hypophysis89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
spinal_cord89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
white_blood_cells89462domestic water buffalowater buffaloBubalus bubalis Description:RNA extracted from snap frozen tissue ...
Analyte type:RNA
Geographic location (latitude and longitude):45.30...
...
+
Blood89462domestic water buffalowater buffaloBubalus bubalis Description:DNA extracted from blood sample of a f...
Analyte type:DNA
Geographic location (latitude and longitude):45.19...
...
+
Displaying 1-10 of 31 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDFile TypeFile FormatSizeRelease Date 
ImageJPG363.37 KB2017-08-23
ReadmeTEXT2.66 KB2017-08-18
otherTEXT0.66 KB2017-08-18
Displaying 11-13 of 13 File(s).

History:

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