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Data from: Genomic structural differences between cattle and River Buffalo identified through comparative genomic and transcriptomic analysis

Water buffalo (Bubalus bubalis L.) is an important livestock species worldwide. Like many other livestock species, water buffalo lacks high quality and continuous reference genome assembly, required for fine-scale comparative genomics studies. In this work, we present a dataset, which characterizes genomic differences between water buffalo genome and the extensively studied cattle (Bos taurus Taurus) reference genome. This data set is obtained after alignment of 14 river buffalo whole genome sequencing datasets to the cattle reference. This data set consisted of 13, 444 deletion CNV regions, and 11,050 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes. Gene expression data from cattle and buffalo were also presented for genes impacted by these regions.

This study sought to characterize differences in gene content, regulation and structure between taurine cattle and river buffalo (2n=50) (one extant type of water buffalo) using the extensively annotated UMD3.1 cattle reference genome as a basis for comparisons. Using 14 WGS datasets from river buffalo, we identified 13,444 deletion CNV regions (Supplemental Table 1) in river buffalo, but not identified in cattle. We also presented 11,050 merged mobile element insertion (MEI) events (Supplemental Table 2) in river buffalo, out of which, 568 of them are within the upstream regions of annotated cattle genes. Furthermore, our tissue transcriptomics analysis provided expression profiles of genes impacted by MEI (Supplemental Tables 3–6) and CNV (Supplemental Table 7) events identified in this study. This data provides the genomic coordinates of identified CNV-deletions and MEI events. Additionally, normalized read count of impacted genes, along with their adjusted p-values of statistical analysis were presented (Supplemental Tables 3–6).

  1. Genomic coordinates of identified CNV-deletion and MEI events, and Ensemble gene names of impacted genes (Supplemental Tables 1 and 2)
  2. Gene expression profiles and statistical significance (adjusted p-values) of genes impacted by MEI in liver (Supplemental Tables 3 and 4)
  3. Gene expression profiles and statistical significance (adjusted p-values) of genes impacted by MEI in muscle (Supplemental Tables 5 and 6)
  4. Gene expression profiles and statistical significance (adjusted p-values) of genes impacted by CNV deletions in river buffalo (Supplemental Table 7)

Public assessment of this dataset will allow for further analyses and functional annotation of genes that are potentially associated with phenotypic difference between cattle and water buffalo. Raw read data of whole genome and transcriptome sequencing were deposited to NCBI Bioprojects.

Dataset Info

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FieldValue
Authors
Li, Wenli
Bickhart, Derick M.
(ORCID)
Ramunno, Luigi
Iamartino, Daniela
(ORCID)
Williams, John L.
(ORCID)
Liu, George E.
(ORCID)
Product Type
Dataset
Intended Use
This dataset will allow for further analyses and functional annotation of genes that are potentially associated with phenotypic difference between cattle and water buffalo. This data presents the major genomic differences between cattle and river buffalo: copy number variation deletion (CNV-deletion) and mobile element insertion (MEI). Genes identified in this analysis provided basis for of further development functional assays aimed at identify genomic factors underlying phenotypic differences between cattle and buffalo. Structural variants and genes identified in this study will facilitate the development of resources suitable for water buffalo genomic selection.
Publisher
Data in Brief
Contact Name
Liu, George E.
Contact Email
Public Access Level
Public
Preferred Dataset Citation
Li, Wenli, Bickhart, Derek M., Ramunno, Luigi, Iamartino, Daniela, Williams, John L. Liu, & George E. (2018). Genomic structural differences between cattle and River Buffalo identified through comparative genomic and transcriptomic analysis. <em>Data in Brief</em> https://doi.org/10.1016/j.dib.2018.05.015
Primary Article

Li, Wenli, Bickhart, Derek M., Ramunno, Luigi, Iamartino, Daniela, Williams, John L. Liu, & George E. (2018). Genomic structural differences between cattle and River Buffalo identified through comparative genomic and transcriptomic analysis. Data in Brief (in press)

Related Article

Li, Wenli, Bickhart, Derek M., Ramunno, Luigi, Iamartino, Daniela, Williams, John L. Liu, & George E. (2018). Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle. Genomics (in press)

Methods Citation

10.1016/j.dib.2018.05.015

License
Funding Source(s)
Agricultural Research Service
5090-31000-024-00-D
Agricultural Research Service
1265-3200-083-00D
Dataset DOI (digital object identifier)
10.1016/j.dib.2018.05.015
Program Code
005:037 - Department of Agriculture - Research and Education
Bureau Code
005:18 - Agricultural Research Service
Modified Date
2019-02-03
Release Date
2018-05-14
Ag Data Commons Keywords: 
  • Genomics & Genetics
  • Transcriptome
  • Genomics & Genetics
  • Genome
  • Genome assembly
  • Animals & Livestock
  • Traits
  • Animals & Livestock
  • Genomics & Genetics
  • Genome
  • Genomics & Genetics
ISO Topic(s):