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cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915659/ https://www.ncbi.nlm.nih.gov/pubmed/27327613 http://dx.doi.org/10.1371/journal.pone.0157779 |
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author | Cartolano, Maria Huettel, Bruno Hartwig, Benjamin Reinhardt, Richard Schneeberger, Korbinian |
author_facet | Cartolano, Maria Huettel, Bruno Hartwig, Benjamin Reinhardt, Richard Schneeberger, Korbinian |
author_sort | Cartolano, Maria |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4915659 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-49156592016-07-06 cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing Cartolano, Maria Huettel, Bruno Hartwig, Benjamin Reinhardt, Richard Schneeberger, Korbinian PLoS One Research Article 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. Public Library of Science 2016-06-21 /pmc/articles/PMC4915659/ /pubmed/27327613 http://dx.doi.org/10.1371/journal.pone.0157779 Text en © 2016 Cartolano et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Cartolano, Maria Huettel, Bruno Hartwig, Benjamin Reinhardt, Richard Schneeberger, Korbinian cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing |
title | cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing |
title_full | cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing |
title_fullStr | cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing |
title_full_unstemmed | cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing |
title_short | cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing |
title_sort | cdna library enrichment of full length transcripts for smrt long read sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915659/ https://www.ncbi.nlm.nih.gov/pubmed/27327613 http://dx.doi.org/10.1371/journal.pone.0157779 |
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