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The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum
Alternative splicing (AS) occurs extensively in eukaryotes as an essential mechanism for regulating transcriptome complexity and diversity, but the AS landscape regulating potassium (K) use efficiency in plants is unclear. In this study, we performed high-throughput transcriptome sequencing of roots...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8630638/ https://www.ncbi.nlm.nih.gov/pubmed/34858465 http://dx.doi.org/10.3389/fpls.2021.774829 |
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author | He, Bing Meng, Lin Tang, Lina Qi, Weicong Hu, Fengqin Lv, Yuanda Song, Wenjing |
author_facet | He, Bing Meng, Lin Tang, Lina Qi, Weicong Hu, Fengqin Lv, Yuanda Song, Wenjing |
author_sort | He, Bing |
collection | PubMed |
description | Alternative splicing (AS) occurs extensively in eukaryotes as an essential mechanism for regulating transcriptome complexity and diversity, but the AS landscape regulating potassium (K) use efficiency in plants is unclear. In this study, we performed high-throughput transcriptome sequencing of roots and shoots from allopolyploid Nicotiana tabacum under K(+) deficiency. Preliminary physiological analysis showed that root system architecture was dramatically changed due to potassium deficiency and that IAA content was significantly reduced in root and shoot. AS analysis showed that a total of 28,179 genes exhibited 54,457 AS events, and 1,510 and 1,732 differentially alternatively spliced (DAS) events were identified in shoots and roots under low K(+) stress. Nevertheless, only 120 DAS events occurred in both shoots and roots, implying that most DAS events were tissue-specific. Both in shoot and the root, the proportion of DAS genes in differentially expressed (DE) genes equaled that in non-DE genes, which indicated that AS might play a unique regulatory role in response to low potassium. Gene ontology analysis further indicated that transcription regulation and AS modulation worked independently in response to low K(+) stress in tobacco, as their target biological processes were different. Totally 45 DAS transcription factors (TFs) were found, which were involved in 18 TF families. Five Auxin response factor (ARF) TFs were significantly DAS in root, suggesting that response to auxin was probably subject to AS regulation in the tobacco root. Our study shows that AS variation occurs extensively and has a particular regulatory mechanism under K(+) deficiency in tobacco. The study also links changes in root system architecture with the changes in AS of ARF TFs, which implied the functional significance of these AS events for root growth and architecture. |
format | Online Article Text |
id | pubmed-8630638 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-86306382021-12-01 The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum He, Bing Meng, Lin Tang, Lina Qi, Weicong Hu, Fengqin Lv, Yuanda Song, Wenjing Front Plant Sci Plant Science Alternative splicing (AS) occurs extensively in eukaryotes as an essential mechanism for regulating transcriptome complexity and diversity, but the AS landscape regulating potassium (K) use efficiency in plants is unclear. In this study, we performed high-throughput transcriptome sequencing of roots and shoots from allopolyploid Nicotiana tabacum under K(+) deficiency. Preliminary physiological analysis showed that root system architecture was dramatically changed due to potassium deficiency and that IAA content was significantly reduced in root and shoot. AS analysis showed that a total of 28,179 genes exhibited 54,457 AS events, and 1,510 and 1,732 differentially alternatively spliced (DAS) events were identified in shoots and roots under low K(+) stress. Nevertheless, only 120 DAS events occurred in both shoots and roots, implying that most DAS events were tissue-specific. Both in shoot and the root, the proportion of DAS genes in differentially expressed (DE) genes equaled that in non-DE genes, which indicated that AS might play a unique regulatory role in response to low potassium. Gene ontology analysis further indicated that transcription regulation and AS modulation worked independently in response to low K(+) stress in tobacco, as their target biological processes were different. Totally 45 DAS transcription factors (TFs) were found, which were involved in 18 TF families. Five Auxin response factor (ARF) TFs were significantly DAS in root, suggesting that response to auxin was probably subject to AS regulation in the tobacco root. Our study shows that AS variation occurs extensively and has a particular regulatory mechanism under K(+) deficiency in tobacco. The study also links changes in root system architecture with the changes in AS of ARF TFs, which implied the functional significance of these AS events for root growth and architecture. Frontiers Media S.A. 2021-11-08 /pmc/articles/PMC8630638/ /pubmed/34858465 http://dx.doi.org/10.3389/fpls.2021.774829 Text en Copyright © 2021 He, Meng, Tang, Qi, Hu, Lv and Song. https://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 | Plant Science He, Bing Meng, Lin Tang, Lina Qi, Weicong Hu, Fengqin Lv, Yuanda Song, Wenjing The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum |
title | The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum |
title_full | The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum |
title_fullStr | The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum |
title_full_unstemmed | The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum |
title_short | The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum |
title_sort | landscape of alternative splicing regulating potassium use efficiency in nicotiana tabacum |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8630638/ https://www.ncbi.nlm.nih.gov/pubmed/34858465 http://dx.doi.org/10.3389/fpls.2021.774829 |
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