Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin

Abstract Background Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°...

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Main Authors: Antanas V. Spokevicius, Josquin Tibbits, Philippe Rigault, Marc-Alexandre Nolin, Caroline Müller, Andrew Merchant
Format: Article
Language:English
Published: BMC 2017-04-01
Series:BMC Genomics
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12864-017-3664-z
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spelling doaj-2514bf2febe3407ab0a1594ee7a002062020-11-25T00:47:06ZengBMCBMC Genomics1471-21642017-04-0118111710.1186/s12864-017-3664-zMedium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental originAntanas V. Spokevicius0Josquin Tibbits1Philippe Rigault2Marc-Alexandre Nolin3Caroline Müller4Andrew Merchant5School of Ecosystem and Forest Sciences, University of MelbourneVictorian AgriBiosciences Centre, La Trobe University R&D ParkGYDLEGYDLEFaculty of Agriculture and the Environment, The University of SydneyFaculty of Agriculture and the Environment, The University of SydneyAbstract Background Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characterizations, little is known regarding gene expression differences that underpin differences in tolerance to environmental change. Using species of contrasting taxonomy, morphology and physiology (E. globulus and E. cladocalyx), this study combines physiological characterizations with ‘second-generation’ sequencing to identify key genes involved in eucalypt responses to medium-term water limitation. Results One hundred twenty Million high-quality HiSeq reads were created from 14 tissue samples in plants that had been successfully subjected to a water deficit treatment or a well-watered control. Alignment to the E. grandis genome saw 23,623 genes of which 468 exhibited differential expression (FDR < 0.01) in one or both ecotypes in response to the treatment. Further analysis identified 80 genes that demonstrated a significant species-specific response of which 74 were linked to the ‘dry’ species E. cladocalyx where 23 of these genes were uncharacterised. The majority (approximately 80%) of these differentially expressed genes, were expressed in stem tissue. Key genes that differentiated species responses were linked to photoprotection/redox balance, phytohormone/signalling, primary photosynthesis/cellular metabolism and secondary metabolism based on plant metabolic pathway network analysis. Conclusion These results highlight a more definitive response to water deficit by a ‘dry’ climate eucalypt, particularly in stem tissue, identifying key pathways and associated genes that are responsible for the differences between ‘wet’ and ‘dry’ climate eucalypts. This knowledge provides the opportunity to further investigate and understand the mechanisms and genetic variation linked to this important environmental response that will assist with genomic efforts in managing native populations as well as in tree improvement programs under future climate scenarios.http://link.springer.com/article/10.1186/s12864-017-3664-zEucalyptusTranscriptomicWater deficitHomeostasisEcotype
collection DOAJ
language English
format Article
sources DOAJ
author Antanas V. Spokevicius
Josquin Tibbits
Philippe Rigault
Marc-Alexandre Nolin
Caroline Müller
Andrew Merchant
spellingShingle Antanas V. Spokevicius
Josquin Tibbits
Philippe Rigault
Marc-Alexandre Nolin
Caroline Müller
Andrew Merchant
Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
BMC Genomics
Eucalyptus
Transcriptomic
Water deficit
Homeostasis
Ecotype
author_facet Antanas V. Spokevicius
Josquin Tibbits
Philippe Rigault
Marc-Alexandre Nolin
Caroline Müller
Andrew Merchant
author_sort Antanas V. Spokevicius
title Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
title_short Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
title_full Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
title_fullStr Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
title_full_unstemmed Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
title_sort medium term water deficit elicits distinct transcriptome responses in eucalyptus species of contrasting environmental origin
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2017-04-01
description Abstract Background Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characterizations, little is known regarding gene expression differences that underpin differences in tolerance to environmental change. Using species of contrasting taxonomy, morphology and physiology (E. globulus and E. cladocalyx), this study combines physiological characterizations with ‘second-generation’ sequencing to identify key genes involved in eucalypt responses to medium-term water limitation. Results One hundred twenty Million high-quality HiSeq reads were created from 14 tissue samples in plants that had been successfully subjected to a water deficit treatment or a well-watered control. Alignment to the E. grandis genome saw 23,623 genes of which 468 exhibited differential expression (FDR < 0.01) in one or both ecotypes in response to the treatment. Further analysis identified 80 genes that demonstrated a significant species-specific response of which 74 were linked to the ‘dry’ species E. cladocalyx where 23 of these genes were uncharacterised. The majority (approximately 80%) of these differentially expressed genes, were expressed in stem tissue. Key genes that differentiated species responses were linked to photoprotection/redox balance, phytohormone/signalling, primary photosynthesis/cellular metabolism and secondary metabolism based on plant metabolic pathway network analysis. Conclusion These results highlight a more definitive response to water deficit by a ‘dry’ climate eucalypt, particularly in stem tissue, identifying key pathways and associated genes that are responsible for the differences between ‘wet’ and ‘dry’ climate eucalypts. This knowledge provides the opportunity to further investigate and understand the mechanisms and genetic variation linked to this important environmental response that will assist with genomic efforts in managing native populations as well as in tree improvement programs under future climate scenarios.
topic Eucalyptus
Transcriptomic
Water deficit
Homeostasis
Ecotype
url http://link.springer.com/article/10.1186/s12864-017-3664-z
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