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

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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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-017-3664-z) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Multi-dimensional scaling plot of transcriptome data distinguishes samples by tissue and species. Multi-dimensional Scaling plot showing the main separation to be between stem derived tissues (Brown) and leaf like tissues (Green) on the x-axis and species (EG – Eucalyptus globulus; EC – E. cladocalyx) on the y-axis
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Fig1: Multi-dimensional scaling plot of transcriptome data distinguishes samples by tissue and species. Multi-dimensional Scaling plot showing the main separation to be between stem derived tissues (Brown) and leaf like tissues (Green) on the x-axis and species (EG – Eucalyptus globulus; EC – E. cladocalyx) on the y-axis

Mentions: Of the 272,167,757 raw reads 240,491,307 passed filtering as high quality (88%; Paired HQ 208,115,303). Of the HQ reads 120,719,749 aligned to 23,623 of the 33,916 annotated E. grandis v1.0 genes and these were used in the differential expression analysis. Most of the remaining reads either aligned to the plastid genomes (Stem Tissues Average 327,506 [3.7%]; Leaf Tissues Average 1,876,819 [24.4%]) or to ribosomal genes (Average 2,044,031 [24%]) with on average 85.5% (s.d. 4.1%) of HQ reads explained per sample (Additional file 1: Dataset S1). Investigation of the unmapped reads indicated these largely derived from unannotated ribosomal genes with ~94.7% of reads explained when mapped to the genome sequence as opposed to annotated genes. A measure of the inter-library variation between replicates (reflecting the biological variability in the data) is the common coefficient of biological variation [28] and was estimated as 0.5711 (Gene-wise estimates ranged from 0.321 to 1.803). A multi-dimensional scaling analysis of the transcriptome data (Fig. 1) shows clear discrimination between the two species and between WW and SS treatments with the tissues clustering by type. This high-level view clearly shows that the physiological differences between the species and treatments, as described above, are reflected in the transcriptome and that the isohydric strategy of E. globulus is reflected in a lesser transcriptome response in all tissues.Fig. 1


Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
Multi-dimensional scaling plot of transcriptome data distinguishes samples by tissue and species. Multi-dimensional Scaling plot showing the main separation to be between stem derived tissues (Brown) and leaf like tissues (Green) on the x-axis and species (EG – Eucalyptus globulus; EC – E. cladocalyx) on the y-axis
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5383985&req=5

Fig1: Multi-dimensional scaling plot of transcriptome data distinguishes samples by tissue and species. Multi-dimensional Scaling plot showing the main separation to be between stem derived tissues (Brown) and leaf like tissues (Green) on the x-axis and species (EG – Eucalyptus globulus; EC – E. cladocalyx) on the y-axis
Mentions: Of the 272,167,757 raw reads 240,491,307 passed filtering as high quality (88%; Paired HQ 208,115,303). Of the HQ reads 120,719,749 aligned to 23,623 of the 33,916 annotated E. grandis v1.0 genes and these were used in the differential expression analysis. Most of the remaining reads either aligned to the plastid genomes (Stem Tissues Average 327,506 [3.7%]; Leaf Tissues Average 1,876,819 [24.4%]) or to ribosomal genes (Average 2,044,031 [24%]) with on average 85.5% (s.d. 4.1%) of HQ reads explained per sample (Additional file 1: Dataset S1). Investigation of the unmapped reads indicated these largely derived from unannotated ribosomal genes with ~94.7% of reads explained when mapped to the genome sequence as opposed to annotated genes. A measure of the inter-library variation between replicates (reflecting the biological variability in the data) is the common coefficient of biological variation [28] and was estimated as 0.5711 (Gene-wise estimates ranged from 0.321 to 1.803). A multi-dimensional scaling analysis of the transcriptome data (Fig. 1) shows clear discrimination between the two species and between WW and SS treatments with the tissues clustering by type. This high-level view clearly shows that the physiological differences between the species and treatments, as described above, are reflected in the transcriptome and that the isohydric strategy of E. globulus is reflected in a lesser transcriptome response in all tissues.Fig. 1

View Article: PubMed Central - PubMed

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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-017-3664-z) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus