DOI: 10.5061/dryad.t40nj78
title: Data from: Challenges and solutions for analyzing dual RNA-seq data for non-model host/pathogen systems

description: 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 and
 reference genome. We performed extensive analyses for a host plant with
 fungal pathogen, and then we extended the plant-fungus results by
 repeating key analyses in vertebrate (human)-fungus and
 vertebrate-bacterium systems. 3. Aligners that were able to map pathogen
 transcripts to the reference genome of a species closely related to the
 pathogen (a “related reference genome”) also mismapped transcripts
 originating from the host to the pathogen’s related reference genome,
 which results in regions where this occurred being quantified as
 overexpressed. If a host reference genome was available, we show that to
 minimize host transcript mismapping while retaining the ability to map
 pathogen transcripts, one could concatenate it with the pathogen’s related
 reference genome, then map transcripts to the concatenated genomes. If a
 host genome was unavailable, assembling reads de novo prior to aligning
 substantially decreased host read mismapping, while retaining the ability
 to map pathogen transcripts to a related reference genome. 4. The
 application of dual RNA-seq to organisms without reference genomes is
 currently limited. We propose an analytical workflow that leverages the
 genomic resources of species closely related to species of interest to
 facilitate application of dual RNA-seq to reveal the mechanisms of
 host-pathogen interactions across a wider array of systems.
description: 76 single-end dual
 RNA-seq simulated sequencing dataset: 1% pathogenSimulated dual RNA-seq
 dataset in which host is Arabidopsis thaliana and pathogen is
 Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end
 reads, and the reads are 1% pathogen and 99% host.76_SE_0.01.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 5% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 5% pathogen and 95% host.76_SE_0.05.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 10% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 10% pathogen and 90% host.76_SE_0.1.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 20% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 20% pathogen and 80% host.76_SE_0.2.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 30% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 30% pathogen and 70% host.76_SE_0.3.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 40% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 40% pathogen and 60% host.76_SE_0.4.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 50% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 50% pathogen and 50% host.76_SE_0.5.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 60% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 60% pathogen and 40% host.76_SE_0.6.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 70% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 70% pathogen and 30% host.76_SE_0.7.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 80% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 80% pathogen and 20% host.76_SE_0.8.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 90% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 90% pathogen and 10% host.76_SE_0.9.fasta.gz76 single-end dual RNA-seq simulated sequencing dataset: 100% pathogenSimulated dual RNA-seq dataset in which host is Arabidopsis thaliana and pathogen is Schizosaccharomyces octosporus. Dataset contains 10 million 76 single-end reads, and the reads are 100% pathogen and 0% host.76_SE_1.0.fasta.gz