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Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.)
The objective of the study is to reveal the freezing tolerance mechanisms of wheat by combining the emerging single-molecule real-time (SMRT) sequencing technology PacBio Sequel and Illumina sequencing. Commercial semiwinter wheat Zhoumai 18 was exposed to −6°C for 4 h at the four-leave stage. Leave...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7300213/ https://www.ncbi.nlm.nih.gov/pubmed/32595694 http://dx.doi.org/10.3389/fgene.2020.00462 |
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author | Zheng, Xingwei Shi, Mengmeng Wang, Jian Yang, Na Wang, Ke Xi, Jilong Wu, Caixia Xi, Tianyuan Zheng, Jun Zhang, Jiancheng |
author_facet | Zheng, Xingwei Shi, Mengmeng Wang, Jian Yang, Na Wang, Ke Xi, Jilong Wu, Caixia Xi, Tianyuan Zheng, Jun Zhang, Jiancheng |
author_sort | Zheng, Xingwei |
collection | PubMed |
description | The objective of the study is to reveal the freezing tolerance mechanisms of wheat by combining the emerging single-molecule real-time (SMRT) sequencing technology PacBio Sequel and Illumina sequencing. Commercial semiwinter wheat Zhoumai 18 was exposed to −6°C for 4 h at the four-leave stage. Leaves of the control group and freezing-treated group were used to perform cDNA library construction. PacBio SMRT sequencing yielded 51,570 high-quality isoforms from leaves of control sample of Zhoumai 18, encoded by 20,366 gene loci. In total, 73,695 transcript isoforms, corresponding to 23,039 genes, were identified from the freezing-treated leaves. Compared with transcripts from the International Wheat Genome Sequencing Consortium RefSeq v1.1, 57,667 novel isoforms were discovered, which were annotated 21,672 known gene loci, as well as 3,399 novel gene loci. Transcriptome characterization including alterative spliced events, alternative polydenylation sites, transcription factors, and fusion transcripts were also analyzed. Freezing-responsive genes and signals were uncovered and proved that the ICE-ERF-COR pathway and ABA signal transduction play a vital role in the freezing response of wheat. In this study, PacBio sequencing and Illumina sequencing were applied to investigate the freezing tolerance in common wheat, and the transcriptome results provide insights into the molecular regulation mechanisms under freezing treatment. |
format | Online Article Text |
id | pubmed-7300213 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-73002132020-06-26 Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.) Zheng, Xingwei Shi, Mengmeng Wang, Jian Yang, Na Wang, Ke Xi, Jilong Wu, Caixia Xi, Tianyuan Zheng, Jun Zhang, Jiancheng Front Genet Genetics The objective of the study is to reveal the freezing tolerance mechanisms of wheat by combining the emerging single-molecule real-time (SMRT) sequencing technology PacBio Sequel and Illumina sequencing. Commercial semiwinter wheat Zhoumai 18 was exposed to −6°C for 4 h at the four-leave stage. Leaves of the control group and freezing-treated group were used to perform cDNA library construction. PacBio SMRT sequencing yielded 51,570 high-quality isoforms from leaves of control sample of Zhoumai 18, encoded by 20,366 gene loci. In total, 73,695 transcript isoforms, corresponding to 23,039 genes, were identified from the freezing-treated leaves. Compared with transcripts from the International Wheat Genome Sequencing Consortium RefSeq v1.1, 57,667 novel isoforms were discovered, which were annotated 21,672 known gene loci, as well as 3,399 novel gene loci. Transcriptome characterization including alterative spliced events, alternative polydenylation sites, transcription factors, and fusion transcripts were also analyzed. Freezing-responsive genes and signals were uncovered and proved that the ICE-ERF-COR pathway and ABA signal transduction play a vital role in the freezing response of wheat. In this study, PacBio sequencing and Illumina sequencing were applied to investigate the freezing tolerance in common wheat, and the transcriptome results provide insights into the molecular regulation mechanisms under freezing treatment. Frontiers Media S.A. 2020-06-11 /pmc/articles/PMC7300213/ /pubmed/32595694 http://dx.doi.org/10.3389/fgene.2020.00462 Text en Copyright © 2020 Zheng, Shi, Wang, Yang, Wang, Xi, Wu, Xi, Zheng and Zhang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Zheng, Xingwei Shi, Mengmeng Wang, Jian Yang, Na Wang, Ke Xi, Jilong Wu, Caixia Xi, Tianyuan Zheng, Jun Zhang, Jiancheng Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.) |
title | Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.) |
title_full | Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.) |
title_fullStr | Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.) |
title_full_unstemmed | Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.) |
title_short | Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.) |
title_sort | isoform sequencing provides insight into freezing response of common wheat (triticum aestivum l.) |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7300213/ https://www.ncbi.nlm.nih.gov/pubmed/32595694 http://dx.doi.org/10.3389/fgene.2020.00462 |
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