Ag Data Commons
Browse

File(s) stored somewhere else

Please note: Linked content is NOT stored on Ag Data Commons and we can't guarantee its availability, quality, security or accept any liability.

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

dataset
posted on 2024-02-13, 13:01 authored by Wenli Li, Derick M. Bickhart, Luigi Ramunno, Daniela Iamartino, John L. Williams, George E. Liu

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.


Resources in this dataset:

  • Resource Title: Genomic structural differences between cattle and River Buffalo identified through comparative genomic and transcriptomic analysis.

    File Name: Web Page, url: https://www.sciencedirect.com/science/article/pii/S2352340918305183

    Data in Brief presenting 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.

    Tables are with this article. Raw read data of whole genome and transcriptome sequencing were deposited to NCBI Bioprojects as the following: PRJNA350833 (https://www.ncbi.nlm.nih.gov/bioproject/?term=350833) PRJNA277147 (https://www.ncbi.nlm.nih.gov/bioproject/?term=277147) PRJEB4351 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB4351)

Funding

USDA-ARS: 5090-31000-024-00-D

USDA-ARS: 1265-3200-083-00D

History

Data contact name

Liu, George E.

Data contact email

George.Liu@ars.usda.gov

Publisher

Data in Brief

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.

Theme

  • Not specified

ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

genomics; cattle; buffaloes; transcriptomics; genes; cattle breeds; phenotype; meat quality; color; prediction; gene expression; sequence alignment; Bubalus bubalis; genome assembly; data collection; genetic variation

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

Primary article PubAg Handle

Pending citation

  • No

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. Data in Brief https://doi.org/10.1016/j.dib.2018.05.015