Sie befinden Sich nicht im Netzwerk der Universität Paderborn. Der Zugriff auf elektronische Ressourcen ist gegebenenfalls nur via VPN oder Shibboleth (DFN-AAI) möglich. mehr Informationen...

Details

Autor(en) / Beteiligte
Titel
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
Ist Teil von
  • Genomics (San Diego, Calif.), 2017-01, Vol.109 (1), p.36-42
Ort / Verlag
United States: Elsevier Inc
Erscheinungsjahr
2017
Link zum Volltext
Quelle
Elsevier ScienceDirect Journals Complete
Beschreibungen/Notizen
  • 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. •Unmapped reads from transcriptome sequencing data can provide information regarding the presence of microorganisms in mammalian samples.•We found that several parasite and virus genome reference assemblies in NCBI were contaminated with bovine DNA.•We confirmed recombination of bovine genomic DNA into BVD virus strains.•De novo assembled contigs of unknown unmapped reads demonstrated incomplete bovine reference genome assemblies.

Weiterführende Literatur

Empfehlungen zum selben Thema automatisch vorgeschlagen von bX