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Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human

BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previou...

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Autores principales: Kuo, Richard I., Tseng, Elizabeth, Eory, Lel, Paton, Ian R., Archibald, Alan L., Burt, David W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404281/
https://www.ncbi.nlm.nih.gov/pubmed/28438136
http://dx.doi.org/10.1186/s12864-017-3691-9
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author Kuo, Richard I.
Tseng, Elizabeth
Eory, Lel
Paton, Ian R.
Archibald, Alan L.
Burt, David W.
author_facet Kuo, Richard I.
Tseng, Elizabeth
Eory, Lel
Paton, Ian R.
Archibald, Alan L.
Burt, David W.
author_sort Kuo, Richard I.
collection PubMed
description BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5′-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences. RESULTS: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5′ cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences. CONCLUSIONS: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3691-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-54042812017-04-27 Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human Kuo, Richard I. Tseng, Elizabeth Eory, Lel Paton, Ian R. Archibald, Alan L. Burt, David W. BMC Genomics Research Article BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5′-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences. RESULTS: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5′ cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences. CONCLUSIONS: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3691-9) contains supplementary material, which is available to authorized users. BioMed Central 2017-04-24 /pmc/articles/PMC5404281/ /pubmed/28438136 http://dx.doi.org/10.1186/s12864-017-3691-9 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Kuo, Richard I.
Tseng, Elizabeth
Eory, Lel
Paton, Ian R.
Archibald, Alan L.
Burt, David W.
Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
title Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
title_full Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
title_fullStr Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
title_full_unstemmed Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
title_short Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
title_sort normalized long read rna sequencing in chicken reveals transcriptome complexity similar to human
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404281/
https://www.ncbi.nlm.nih.gov/pubmed/28438136
http://dx.doi.org/10.1186/s12864-017-3691-9
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