title: Unmapped reads from cattle RNAseq data: A source for missing and misassembled sequences in the reference assemblies and for detection of pathogens in the host.
abstract: Usually, reads from transcriptome sequencing data unmapped to the target species' reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double-stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response. Alignment data also demonstrated incomplete bovine reference genome assemblies. In addition, we found that several parasite and virus genome reference assemblies in NCBI were contaminated with bovine DNA and confirmed recombination of bovine DNA into BVD virus strains. Exploring unmapped reads can extract useful biological information regarding the presence of microorganisms and can highlight issues with reference genome assemblies of host and pathogen species.
authors.affiliation: Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany; College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan 23200, Pakistan.
authors.forename: Tahir
authors.initials: T
authors.lastname: Usman
authors.affiliation: Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany.
authors.forename: Frieder
authors.initials: F
authors.lastname: Hadlich
authors.affiliation: Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany.
authors.forename: Wiebke
authors.initials: W
authors.lastname: Demasius
authors.affiliation: Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany.
authors.forename: Rosemarie
authors.initials: R
authors.lastname: Weikard
authors.affiliation: Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany; Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany. Electronic address: kuehn@fbn-dummerstorf.de.
authors.forename: Christa
authors.initials: C
authors.lastname: Kühn
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics* / Q000382:microbiology / Q000469:parasitology / Q000821:virology; D019295:Computational Biology; D005260:Female; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards*; D017423:Sequence Analysis, RNA / Q000592:standards*
keywords: Bioinformatics; Next generation sequencing; RNAseq; Unmapped reads