Transcriptome Analysis in Domesticated Species – Challenges and Strategies

Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, the authors discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.

RNA-seq bioinformatic workflow for calling differentially expressed genes

1. Remove low-quality reads, barcodes, and adapters Fastx-toolkit, FLEXBAR, or Trimmomatic Follow recommended protocol
2. Remove mitochondrial and ribosomal sequences Bowtie2 Sequences from the same or related species should be used
3. Align to reference genome TopHat2 Incomplete or nonexistent reference genome
4. Call differentially expressed genes DESeq2, edgeR, or limma Incomplete or nonexistent reference genome annotation


Hekman JP, Johnson JL, Kukekova AV. (2016) Transcriptome Analysis in Domesticated Species: Challenges and Strategies. Bioinform Biol Insights 9(Suppl 4):21-31. [article]

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