Exploring the unmapped DNA and RNA reads in a songbird genome

Laine VN, Goßmann T, van Oers K, Visser ME, Groenen MAM (2018)
bioRxiv.

Preprint | Veröffentlicht | Englisch
 
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Autor*in
Laine, Veronika N.; Goßmann, ToniUniBi ; van Oers, Kees; Visser, Marcel E.; Groenen, Martien A.M.
Abstract / Bemerkung
AbstractBackgroundA widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. A significant percentage of reads, however, frequently remain unmapped despite improvements in the methods and hardware, which have enhanced the efficiency and accuracy of alignments. Usually unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from this data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies. The generated sequence contigs were then aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.ResultsMany of the aligned contigs showed sequence similarity to sequences from different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.ConclusionsOur analyses revealed that meaningful biological information can be found when further exploring unmapped reads. It is possible to discover sequences that are either absent or misassembled in the reference genome and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.
Erscheinungsjahr
2018
Zeitschriftentitel
bioRxiv
Page URI
https://pub.uni-bielefeld.de/record/2941288

Zitieren

Laine VN, Goßmann T, van Oers K, Visser ME, Groenen MAM. Exploring the unmapped DNA and RNA reads in a songbird genome. bioRxiv. 2018.
Laine, V. N., Goßmann, T., van Oers, K., Visser, M. E., & Groenen, M. A. M. (2018). Exploring the unmapped DNA and RNA reads in a songbird genome. bioRxiv
Laine, V. N., Goßmann, T., van Oers, K., Visser, M. E., and Groenen, M. A. M. (2018). Exploring the unmapped DNA and RNA reads in a songbird genome. bioRxiv.
Laine, V.N., et al., 2018. Exploring the unmapped DNA and RNA reads in a songbird genome. bioRxiv.
V.N. Laine, et al., “Exploring the unmapped DNA and RNA reads in a songbird genome”, bioRxiv, 2018.
Laine, V.N., Goßmann, T., van Oers, K., Visser, M.E., Groenen, M.A.M.: Exploring the unmapped DNA and RNA reads in a songbird genome. bioRxiv. (2018).
Laine, Veronika N., Goßmann, Toni, van Oers, Kees, Visser, Marcel E., and Groenen, Martien A.M. “Exploring the unmapped DNA and RNA reads in a songbird genome”. bioRxiv (2018).

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Preprint: 10.1101/371963

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