title: Issues with RNA-seq analysis in non-model organisms: A salmonid example.
abstract: High throughput sequencing (HTS) is useful for many purposes as exemplified by the other topics included in this special issue. The purpose of this paper is to look into the unique challenges of using this technology in non-model organisms where resources such as genomes, functional genome annotations or genome complexity provide obstacles not met in model organisms. To describe these challenges, we narrow our scope to RNA sequencing used to study differential gene expression in response to pathogen challenge. As a demonstration species we chose Atlantic salmon, which has a sequenced genome with poor annotation and an added complexity due to many duplicated genes. We find that our RNA-seq analysis pipeline deciphers between duplicates despite high sequence identity. However, annotation issues provide problems in linking differentially expressed genes to pathways. Also, comparing results between approaches and species are complicated due to lack of standardized annotation.
authors.affiliation: Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway.
authors.forename: Arvind
authors.initials: A
authors.lastname: Sundaram
authors.affiliation: Norwegian Veterinary Institute, Department of Virology, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
authors.forename: Torstein
authors.initials: T
authors.lastname: Tengs
authors.affiliation: Norwegian Veterinary Institute, Department of Virology, P.O. Box 750 Sentrum, 0106 Oslo, Norway. Electronic address: Unni.Grimholt@vetinst.no.
authors.forename: Unni
authors.initials: U
authors.lastname: Grimholt
mesh_terms: D000818:Animals; D019992:Databases as Topic; D020869:Gene Expression Profiling; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054884:Host-Pathogen Interactions / Q000235:genetics; D007113:Immunity, Innate; D058977:Molecular Sequence Annotation; D012015:Reference Standards; D012487:Salmonidae / Q000235:genetics* / Q000276:immunology; D015398:Signal Transduction
keywords: Comparative immunology; Genomics; High throughput sequencing; RNA-seq analyses