Abstract
New and improved assemblies for bovine genomes have been released in the past two years, contributing to the growing field of livestock genomic information, but they still require to be more comprehensively evaluated in RNA-seq bioinformatic pipelines in terms of their reproducibility in mapping and differential gene expression analysis. The present study aimed to evaluate these parameters by mapping Brangus-derived leukocyte sequence data to three bovine reference genome assemblies (Hereford, Brahman, and Angus) in order to find differentially expressed genes related to ectoparasite host resistance. We observed similar mapping rates across the three genome assemblies and a similar number of differentially expressed genes (DEGs) detected with each genome (84-86 genes). However, using haplotype-resolved genomes (Angus and Brahman) was found to be important to discover an additional 45 DEGs that could not be identified with the non−haplotype-resolved Hereford reference genome.
| Original language | English |
|---|---|
| Title of host publication | Proceedings of the 24th Association for the Advancement of Animal Breeding and Genetics Conference |
| Place of Publication | Armidale, Austra |
| Pages | 222-225 |
| Publication status | Published - 30 Nov 2021 |
Fingerprint
Dive into the research topics of 'Effect of bovine reference genome choice in RNA-SEQ alignment and differential gene expression analysis in Brangus cattle'. Together they form a unique fingerprint.Cite this
- APA
- Author
- BIBTEX
- Harvard
- Standard
- RIS
- Vancouver