Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Background: Consuming watercress is thought to provide health benefits as a consequence of its phytonutrient composition. However, for watercress there are currently limited genetic resources underpinning breeding efforts for either yield or phytonutritional traits. In this paper, we use RNASeq data from twelve watercress accessions to characterize the transcriptome, perform candidate gene mining and conduct differential expression analysis for two key phytonutritional traits: antioxidant (AO) capacity and glucosinolate (GLS) content.
Results: The watercress transcriptome was assembled to 80,800 transcripts (48,732 unigenes); 71 % of which were annotated based on orthology to Arabidopsis. Differential expression analysis comparing watercress accessions with ‘high’ and ‘low’ AO and GLS resulted in 145 and 94 differentially expressed loci for AO capacity and GLS respectively. Differentially expressed loci between high and low AO watercress were significantly enriched for genes involved in plant defence and response to stimuli, in line with the observation that AO are involved in plant stress-response. Differential expression between the high and low GLS watercress identified links to GLS regulation and also novel transcripts warranting further investigation. Additionally, we successfully identified watercress orthologs for Arabidopsis phenylpropanoid, GLS and shikimate biosynthesis pathway genes, and compiled a catalogue of polymorphic markers for future applications.
Conclusions: Our work describes the first transcriptome of watercress and establishes the foundation for further molecular study by providing valuable resources, including sequence data, annotated transcripts, candidate genes and markers.
watercress, nasturtium officinale, brassicaceae, RNASeq, de novo assembly, differential expression, antioxidant capacity, glucosinolates, gluconasturtiin, phenylpropanoid pathway
1-15
Voutsina, Nikol
68a57328-0a4b-4f72-a17d-d3e77f7240f7
Payne, Adrienne C.
b7b4bce0-e6e5-4bfe-a220-a1eaac9ca17c
Hancock, Robert D.
f11a14de-369e-42e7-89ce-7cca55a5e4f4
Clarkson, Graham J.J.
ef06b7b4-509b-4ebe-9327-c8950c4f44b3
Rothwell, Steve D.
bb161dcf-d9fc-4334-b04d-28d385e3925b
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
20 May 2016
Voutsina, Nikol
68a57328-0a4b-4f72-a17d-d3e77f7240f7
Payne, Adrienne C.
b7b4bce0-e6e5-4bfe-a220-a1eaac9ca17c
Hancock, Robert D.
f11a14de-369e-42e7-89ce-7cca55a5e4f4
Clarkson, Graham J.J.
ef06b7b4-509b-4ebe-9327-c8950c4f44b3
Rothwell, Steve D.
bb161dcf-d9fc-4334-b04d-28d385e3925b
Chapman, Mark
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Voutsina, Nikol, Payne, Adrienne C., Hancock, Robert D., Clarkson, Graham J.J., Rothwell, Steve D., Chapman, Mark and Taylor, Gail
(2016)
Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health.
BMC Genomics, 17 (378), .
(doi:10.1186/s12864-016-2704-4).
Abstract
Background: Consuming watercress is thought to provide health benefits as a consequence of its phytonutrient composition. However, for watercress there are currently limited genetic resources underpinning breeding efforts for either yield or phytonutritional traits. In this paper, we use RNASeq data from twelve watercress accessions to characterize the transcriptome, perform candidate gene mining and conduct differential expression analysis for two key phytonutritional traits: antioxidant (AO) capacity and glucosinolate (GLS) content.
Results: The watercress transcriptome was assembled to 80,800 transcripts (48,732 unigenes); 71 % of which were annotated based on orthology to Arabidopsis. Differential expression analysis comparing watercress accessions with ‘high’ and ‘low’ AO and GLS resulted in 145 and 94 differentially expressed loci for AO capacity and GLS respectively. Differentially expressed loci between high and low AO watercress were significantly enriched for genes involved in plant defence and response to stimuli, in line with the observation that AO are involved in plant stress-response. Differential expression between the high and low GLS watercress identified links to GLS regulation and also novel transcripts warranting further investigation. Additionally, we successfully identified watercress orthologs for Arabidopsis phenylpropanoid, GLS and shikimate biosynthesis pathway genes, and compiled a catalogue of polymorphic markers for future applications.
Conclusions: Our work describes the first transcriptome of watercress and establishes the foundation for further molecular study by providing valuable resources, including sequence data, annotated transcripts, candidate genes and markers.
Text
Voutsina_2015_WatercressRNASeq.pdf
- Accepted Manuscript
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art_10.1186_s12864-016-2704-4.pdf
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Supplement_Figure_S1.pdf
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More information
Accepted/In Press date: 4 May 2016
e-pub ahead of print date: 20 May 2016
Published date: 20 May 2016
Keywords:
watercress, nasturtium officinale, brassicaceae, RNASeq, de novo assembly, differential expression, antioxidant capacity, glucosinolates, gluconasturtiin, phenylpropanoid pathway
Organisations:
Centre for Biological Sciences
Identifiers
Local EPrints ID: 394514
URI: http://eprints.soton.ac.uk/id/eprint/394514
ISSN: 1471-2164
PURE UUID: 60aa3dbf-42be-404a-9a41-786966fb9886
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Date deposited: 16 May 2016 14:23
Last modified: 21 Nov 2024 02:45
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Contributors
Author:
Nikol Voutsina
Author:
Adrienne C. Payne
Author:
Robert D. Hancock
Author:
Graham J.J. Clarkson
Author:
Steve D. Rothwell
Author:
Gail Taylor
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