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Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing
BACKGROUND: Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-gen...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214230/ https://www.ncbi.nlm.nih.gov/pubmed/30397543 http://dx.doi.org/10.7717/peerj.5818 |
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author | Piriyapongsa, Jittima Kaewprommal, Pavita Vaiwsri, Sirintra Anuntakarun, Songtham Wirojsirasak, Warodom Punpee, Prapat Klomsa-ard, Peeraya Shaw, Philip J. Pootakham, Wirulda Yoocha, Thippawan Sangsrakru, Duangjai Tangphatsornruang, Sithichoke Tongsima, Sissades Tragoonrung, Somvong |
author_facet | Piriyapongsa, Jittima Kaewprommal, Pavita Vaiwsri, Sirintra Anuntakarun, Songtham Wirojsirasak, Warodom Punpee, Prapat Klomsa-ard, Peeraya Shaw, Philip J. Pootakham, Wirulda Yoocha, Thippawan Sangsrakru, Duangjai Tangphatsornruang, Sithichoke Tongsima, Sissades Tragoonrung, Somvong |
author_sort | Piriyapongsa, Jittima |
collection | PubMed |
description | BACKGROUND: Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs. METHODS: We generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors. RESULTS: A total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants. DISCUSSION: The new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar. |
format | Online Article Text |
id | pubmed-6214230 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-62142302018-11-05 Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing Piriyapongsa, Jittima Kaewprommal, Pavita Vaiwsri, Sirintra Anuntakarun, Songtham Wirojsirasak, Warodom Punpee, Prapat Klomsa-ard, Peeraya Shaw, Philip J. Pootakham, Wirulda Yoocha, Thippawan Sangsrakru, Duangjai Tangphatsornruang, Sithichoke Tongsima, Sissades Tragoonrung, Somvong PeerJ Agricultural Science BACKGROUND: Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs. METHODS: We generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors. RESULTS: A total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants. DISCUSSION: The new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar. PeerJ Inc. 2018-10-30 /pmc/articles/PMC6214230/ /pubmed/30397543 http://dx.doi.org/10.7717/peerj.5818 Text en ©2018 Piriyapongsa 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, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Agricultural Science Piriyapongsa, Jittima Kaewprommal, Pavita Vaiwsri, Sirintra Anuntakarun, Songtham Wirojsirasak, Warodom Punpee, Prapat Klomsa-ard, Peeraya Shaw, Philip J. Pootakham, Wirulda Yoocha, Thippawan Sangsrakru, Duangjai Tangphatsornruang, Sithichoke Tongsima, Sissades Tragoonrung, Somvong Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing |
title | Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing |
title_full | Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing |
title_fullStr | Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing |
title_full_unstemmed | Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing |
title_short | Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing |
title_sort | uncovering full-length transcript isoforms of sugarcane cultivar khon kaen 3 using single-molecule long-read sequencing |
topic | Agricultural Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214230/ https://www.ncbi.nlm.nih.gov/pubmed/30397543 http://dx.doi.org/10.7717/peerj.5818 |
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