Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress
BACKGROUND: The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has become an important objective for crop improvement. Some wild crop relatives h...
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ftpubmed:oai:pubmedcentral.nih.gov:7278158 2023-05-15T15:14:06+02:00 Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress Simopoulos, Caitlin M. A. MacLeod, Mitchell J. R. Irani, Solmaz Sung, Wilson W. L. Champigny, Marc J. Summers, Peter S. Golding, G. Brian Weretilnyk, Elizabeth A. 2020-06-08 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7278158/ http://www.ncbi.nlm.nih.gov/pubmed/32513102 https://doi.org/10.1186/s12864-020-06793-7 en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7278158/ http://www.ncbi.nlm.nih.gov/pubmed/32513102 http://dx.doi.org/10.1186/s12864-020-06793-7 © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data. CC0 PDM CC-BY BMC Genomics Research Article Text 2020 ftpubmed https://doi.org/10.1186/s12864-020-06793-7 2020-06-14T00:41:14Z BACKGROUND: The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has become an important objective for crop improvement. Some wild crop relatives have adapted to extreme osmotic stresses and can provide valuable insights into traits and genetic signatures that can guide efforts to improve crop tolerance to water deficits. Eutrema salsugineum, a close relative of many cruciferous crops, is a halophytic plant and extremophyte model for abiotic stress research. RESULTS: Using comparative transcriptomics, we show that two E. salsugineum ecotypes display significantly different transcriptional responses towards a two-stage drought treatment. Even before visibly wilting, water deficit led to the differential expression of almost 1,100 genes for an ecotype from the semi-arid, sub-arctic Yukon, Canada, but only 63 genes for an ecotype from the semi-tropical, monsoonal, Shandong, China. After recovery and a second drought treatment, about 5,000 differentially expressed genes were detected in Shandong plants versus 1,900 genes in Yukon plants. Only 13 genes displayed similar drought-responsive patterns for both ecotypes. We detected 1,007 long non-protein coding RNAs (lncRNAs), 8% were only expressed in stress-treated plants, a surprising outcome given the documented association between lncRNA expression and stress. Co-expression network analysis of the transcriptomes identified eight gene clusters where at least half of the genes in each cluster were differentially expressed. While many gene clusters were correlated to drought treatments, only a single cluster significantly correlated to drought exposure in both ecotypes. CONCLUSION: Extensive, ecotype-specific transcriptional reprogramming with drought was unexpected given that both ecotypes are adapted to saline habitats providing persistent exposure to osmotic stress. This ecotype-specific response would have escaped ... Text Arctic Yukon PubMed Central (PMC) Arctic Canada Yukon BMC Genomics 21 1 |
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Research Article Simopoulos, Caitlin M. A. MacLeod, Mitchell J. R. Irani, Solmaz Sung, Wilson W. L. Champigny, Marc J. Summers, Peter S. Golding, G. Brian Weretilnyk, Elizabeth A. Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress |
topic_facet |
Research Article |
description |
BACKGROUND: The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has become an important objective for crop improvement. Some wild crop relatives have adapted to extreme osmotic stresses and can provide valuable insights into traits and genetic signatures that can guide efforts to improve crop tolerance to water deficits. Eutrema salsugineum, a close relative of many cruciferous crops, is a halophytic plant and extremophyte model for abiotic stress research. RESULTS: Using comparative transcriptomics, we show that two E. salsugineum ecotypes display significantly different transcriptional responses towards a two-stage drought treatment. Even before visibly wilting, water deficit led to the differential expression of almost 1,100 genes for an ecotype from the semi-arid, sub-arctic Yukon, Canada, but only 63 genes for an ecotype from the semi-tropical, monsoonal, Shandong, China. After recovery and a second drought treatment, about 5,000 differentially expressed genes were detected in Shandong plants versus 1,900 genes in Yukon plants. Only 13 genes displayed similar drought-responsive patterns for both ecotypes. We detected 1,007 long non-protein coding RNAs (lncRNAs), 8% were only expressed in stress-treated plants, a surprising outcome given the documented association between lncRNA expression and stress. Co-expression network analysis of the transcriptomes identified eight gene clusters where at least half of the genes in each cluster were differentially expressed. While many gene clusters were correlated to drought treatments, only a single cluster significantly correlated to drought exposure in both ecotypes. CONCLUSION: Extensive, ecotype-specific transcriptional reprogramming with drought was unexpected given that both ecotypes are adapted to saline habitats providing persistent exposure to osmotic stress. This ecotype-specific response would have escaped ... |
format |
Text |
author |
Simopoulos, Caitlin M. A. MacLeod, Mitchell J. R. Irani, Solmaz Sung, Wilson W. L. Champigny, Marc J. Summers, Peter S. Golding, G. Brian Weretilnyk, Elizabeth A. |
author_facet |
Simopoulos, Caitlin M. A. MacLeod, Mitchell J. R. Irani, Solmaz Sung, Wilson W. L. Champigny, Marc J. Summers, Peter S. Golding, G. Brian Weretilnyk, Elizabeth A. |
author_sort |
Simopoulos, Caitlin M. A. |
title |
Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress |
title_short |
Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress |
title_full |
Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress |
title_fullStr |
Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress |
title_full_unstemmed |
Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress |
title_sort |
coding and long non-coding rnas provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant eutrema salsugineum undergoing water deficit stress |
publisher |
BioMed Central |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7278158/ http://www.ncbi.nlm.nih.gov/pubmed/32513102 https://doi.org/10.1186/s12864-020-06793-7 |
geographic |
Arctic Canada Yukon |
geographic_facet |
Arctic Canada Yukon |
genre |
Arctic Yukon |
genre_facet |
Arctic Yukon |
op_source |
BMC Genomics |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7278158/ http://www.ncbi.nlm.nih.gov/pubmed/32513102 http://dx.doi.org/10.1186/s12864-020-06793-7 |
op_rights |
© The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data. |
op_rightsnorm |
CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s12864-020-06793-7 |
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BMC Genomics |
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21 |
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