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
Abstract 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 rel...
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ftdatacite:10.6084/m9.figshare.c.5013047 2023-05-15T15:19:06+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. G. Brian Golding Weretilnyk, Elizabeth A. 2020 https://dx.doi.org/10.6084/m9.figshare.c.5013047 https://springernature.figshare.com/collections/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/5013047 unknown figshare https://dx.doi.org/10.1186/s12864-020-06793-7 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Genetics FOS Biological sciences Plant Biology Collection article 2020 ftdatacite https://doi.org/10.6084/m9.figshare.c.5013047 https://doi.org/10.1186/s12864-020-06793-7 2021-11-05T12:55:41Z Abstract 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 notice had we used a single exposure to water deficit. Finally, the apparent capacity to improve tolerance and growth after a drought episode represents an important adaptive trait for a plant that thrives under semi-arid Yukon conditions, and may be similarly advantageous for crop species experiencing stresses attributed to climate change. Article in Journal/Newspaper Arctic Climate change Yukon DataCite Metadata Store (German National Library of Science and Technology) Arctic Yukon Canada |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Genetics FOS Biological sciences Plant Biology |
spellingShingle |
Genetics FOS Biological sciences Plant Biology Simopoulos, Caitlin M. A. MacLeod, Mitchell J. R. Irani, Solmaz Sung, Wilson W. L. Champigny, Marc J. Summers, Peter S. G. Brian Golding 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 |
Genetics FOS Biological sciences Plant Biology |
description |
Abstract 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 notice had we used a single exposure to water deficit. Finally, the apparent capacity to improve tolerance and growth after a drought episode represents an important adaptive trait for a plant that thrives under semi-arid Yukon conditions, and may be similarly advantageous for crop species experiencing stresses attributed to climate change. |
format |
Article in Journal/Newspaper |
author |
Simopoulos, Caitlin M. A. MacLeod, Mitchell J. R. Irani, Solmaz Sung, Wilson W. L. Champigny, Marc J. Summers, Peter S. G. Brian Golding 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. G. Brian Golding 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 |
figshare |
publishDate |
2020 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.5013047 https://springernature.figshare.com/collections/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/5013047 |
geographic |
Arctic Yukon Canada |
geographic_facet |
Arctic Yukon Canada |
genre |
Arctic Climate change Yukon |
genre_facet |
Arctic Climate change Yukon |
op_relation |
https://dx.doi.org/10.1186/s12864-020-06793-7 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.5013047 https://doi.org/10.1186/s12864-020-06793-7 |
_version_ |
1766349294515781632 |