Challenges and solutions for analyzing dual RNA-seq data for non-model host/pathogen systems

1. Dual RNA-seq simultaneously profiles the transcriptomes of a host and pathogen during infection and may reveal the mechanisms underlying host-pathogen interactions. Dual RNA-seq is inherently a mixture of transcripts from at least two species (host and pathogen), so this mixture must be computationally sorted into host and pathogen components. Sorting relies on aligning reads to respective reference genomes, which may be unavailable for both species in non-model host-pathogen pairs. This lack of genomic resources may present challenges to applying dual RNA-seq to non-model systems. 2. We assessed the accuracy of alignments of dual RNA-seq when using the genomic resources of a closely-related species to the species of interest by simulating datasets of mixed transcripts from a host and pathogen. Specifically, we compared how different aligners performed across different proportions of pathogen to host transcripts and across variation in the genetic distance between the pathogen genome...