Figure 1.

Challenges of homoeolog gene expression analysis. (A) Using the allotetraploid cotton species as an example, only a small portion of RNA-seq reads contain diagnostic SNPs (i.e. homoeolog-specific reads) reflecting the parental origin of homoeologous genes. (B) An analytic workflow of RNA-seq analysis was applied to evaluate the use of homoeolog-specific reads to study duplicated gene expression and co-expression networks. A ground-truth, in silico dataset of allopolyploid cotton (AD) was generated from the parental diploid cotton A₂ and D₅ reads, which was analyzed using a variety of method choices.