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Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing
BACKGROUND: Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternative...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009963/ https://www.ncbi.nlm.nih.gov/pubmed/29951114 http://dx.doi.org/10.1186/s13068-018-1167-z |
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author | Zuo, Chunman Blow, Matthew Sreedasyam, Avinash Kuo, Rita C. Ramamoorthy, Govindarajan Kunde Torres-Jerez, Ivone Li, Guifen Wang, Mei Dilworth, David Barry, Kerrie Udvardi, Michael Schmutz, Jeremy Tang, Yuhong Xu, Ying |
author_facet | Zuo, Chunman Blow, Matthew Sreedasyam, Avinash Kuo, Rita C. Ramamoorthy, Govindarajan Kunde Torres-Jerez, Ivone Li, Guifen Wang, Mei Dilworth, David Barry, Kerrie Udvardi, Michael Schmutz, Jeremy Tang, Yuhong Xu, Ying |
author_sort | Zuo, Chunman |
collection | PubMed |
description | BACKGROUND: Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. RESULTS: We present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon–intron structures. CONCLUSIONS: Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13068-018-1167-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6009963 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60099632018-06-27 Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing Zuo, Chunman Blow, Matthew Sreedasyam, Avinash Kuo, Rita C. Ramamoorthy, Govindarajan Kunde Torres-Jerez, Ivone Li, Guifen Wang, Mei Dilworth, David Barry, Kerrie Udvardi, Michael Schmutz, Jeremy Tang, Yuhong Xu, Ying Biotechnol Biofuels Research BACKGROUND: Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. RESULTS: We present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon–intron structures. CONCLUSIONS: Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13068-018-1167-z) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-20 /pmc/articles/PMC6009963/ /pubmed/29951114 http://dx.doi.org/10.1186/s13068-018-1167-z Text en © The Author(s) 2018 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 Zuo, Chunman Blow, Matthew Sreedasyam, Avinash Kuo, Rita C. Ramamoorthy, Govindarajan Kunde Torres-Jerez, Ivone Li, Guifen Wang, Mei Dilworth, David Barry, Kerrie Udvardi, Michael Schmutz, Jeremy Tang, Yuhong Xu, Ying Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing |
title | Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing |
title_full | Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing |
title_fullStr | Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing |
title_full_unstemmed | Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing |
title_short | Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing |
title_sort | revealing the transcriptomic complexity of switchgrass by pacbio long-read sequencing |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009963/ https://www.ncbi.nlm.nih.gov/pubmed/29951114 http://dx.doi.org/10.1186/s13068-018-1167-z |
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