Universität zu Köln

Cartolano, Maria ORCID: 0000-0001-9830-988X, Huettel, Bruno, Hartwig, Benjamin, Reinhardt, Richard ORCID: 0000-0001-9376-2132 and Schneeberger, Korbinian (2016). cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing. PLoS One, 11 (6). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

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Abstract

The utility of genome assemblies does not only rely on the quality of the assembled genome sequence, but also on the quality of the gene annotations. The Pacific Biosciences Iso-Seq technology is a powerful support for accurate eukaryotic gene model annotation as it allows for direct readout of full-length cDNA sequences without the need for noisy short read-based transcript assembly. We propose the implementation of the TeloPrime Full Length cDNA Amplification kit to the Pacific Biosciences Iso-Seq technology in order to enrich for genuine full-length transcripts in the cDNA libraries. We provide evidence that TeloPrime outperforms the commonly used SMARTer PCR cDNA Synthesis Kit in identifying transcription start and end sites in Arabidopsis thaliana. Furthermore, we show that TeloPrime-based Pacific Biosciences Iso-Seq can be successfully applied to the polyploid genome of bread wheat (Triticum aestivum) not only to efficiently annotate gene models, but also to identify novel transcription sites, gene homeologs, splicing isoforms and previously unidentified gene loci.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Cartolano, Maria UNSPECIFIED orcid.org/0000-0001-9830-988X UNSPECIFIED Huettel, Bruno UNSPECIFIED UNSPECIFIED UNSPECIFIED Hartwig, Benjamin UNSPECIFIED UNSPECIFIED UNSPECIFIED Reinhardt, Richard UNSPECIFIED orcid.org/0000-0001-9376-2132 UNSPECIFIED Schneeberger, Korbinian UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-272113
DOI:	10.1371/journal.pone.0157779
Journal or Publication Title:	PLoS One
Volume:	11
Number:	6
Date:	2016
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1932-6203
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language RNA-SEQ; RECONSTRUCTION Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/27211