Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress

Nah, Gyoungju; Lee, Moonsub; Kim, Do Soon; Rayburn, A. Lane; Voigt, Thomas; Lee, D. K.

doi:10.1371/journal.pone.0152294

Cited by 19 publications

(9 citation statements)

References 85 publications

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“…With the development of next-generation sequencing (NGS) technology, large scale transcriptome data has become availavle in various species [ 4 ]. In recent years, Illumina RNA-Seq technology has been successfully applied to many plant species, such as Beta vulgaris [ 5 ], Spartina pectinata [ 6 ], Camellia sinensis [ 7 ], Lilium lancifolium [ 8 ], and Camellia japonica [ 9 ], for its high accuracy and sensitivity of gene discovery.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

et al. 2018

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BackgroundChrysanthemum is one kind of ornamental plant well-known and widely used in the world. However, its quality and production were severely affected by low temperature conditions in winter and early spring periods. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze chrysanthemum (Dendranthema grandiflorum) transcription response to low temperature.ResultsUsing Illumina sequencing technology, a total of 86,444,237 high-quality clean reads and 93,837 unigenes were generated from four libraries: T01, controls; T02, 4 °C cold acclimation (CA) for 24 h; T03, − 4 °C freezing treatments for 4 h with prior CA; and T04, − 4 °C freezing treatments for 4 h without prior CA. In total, 7583 differentially expressed genes (DEGs) of 36,462 annotated unigenes were identified. We performed GO and KEGG pathway enrichment analyses, and excavated a group of important cold-responsive genes related to low temperature sensing and signal transduction, membrane lipid stability, reactive oxygen species (ROS) scavenging and osmoregulation. These genes encode many key proteins in plant biological processes, such as protein kinases, transcription factors, fatty acid desaturase, lipid-transfer proteins, antifreeze proteins, antioxidase and soluble sugars synthetases. We also verified expression levels of 10 DEGs using quantitative real-time polymerase chain reaction (qRT-PCR). In addition, we performed the determination of physiological indicators of chrysanthemum treated at low temperature, and the results were basically consistent with molecular sequencing results.ConclusionIn summary, our study presents a genome-wide transcript profile of Dendranthema grandiflorum var. jinba and provides insights into the molecular mechanisms of D. grandiflorum in response to low temperature. These data contributes to our deeper relevant researches on cold tolerance and further exploring new candidate genes for chilling-tolerance and freezing-tolerance chrysanthemum molecular breeding.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4706-x) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

et al. 2018

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“…Our data are also consistent with studies examining other DNA repair genes (although not the ones included in this study) under cold stress. At least two genes coding for enzymes involved in repair of UV‐induced damage are known to be freezing‐inducible (Bae et al, 2003; Dong et al, 2014), as is one involved in translesion synthesis (Nah et al, 2016), and increased DNA ligase activity may be linked to seed viability under cold stress in Arabidopsis (Waterworth et al, 2010). One unexpected note was our negative results with respect to stress effects on RAD‐23 .…”

Section: Discussionmentioning

confidence: 99%

“…Some experimental findings support this hypothesis. Low temperature (either freezing or chilling) is associated with increased expression of the excision repair gene RAD‐23 in Arabidopsis (Kawamura and Uemura, 2003), the translesion synthesis gene REV3 in Spartina pectinata (Nah et al, 2016), and the excision repair enzyme DRT102 (involved in repair of UV‐induced damage) in Arabidopsis (Bae et al, 2003) and Brassica rapa (Dong et al, 2014). However, much work remains to be done to explore how other genes involved in DNA damage repair might respond to freezing stress and whether DNA damage repair in perennial plants is affected by age.…”

Section: Abbreviationsmentioning

confidence: 99%

Nucleic acid damage and DNA repair are affected by freezing stress in annual wheat (Triticum aestivum) and by plant age and freezing in its perennial relative (Thinopyrum intermedium)

Jaikumar

Dorn

Baas

et al. 2020

American J of Botany

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PREMISE Nucleic acid integrity can be compromised under many abiotic stresses. To date, however, few studies have considered whether nucleic acid damage and damage repair play a role in cold‐stress adaptation. A further insufficiently explored question concerns how age affects cold stress adaptation among mature perennials. As a plant ages, the optimal trade‐off between growth and stress tolerance may shift. METHODS Oxidative damage to RNA and expression of genes involved in DNA repair were compared in multiple mature cohorts of Thinopyrum intermedium (an emerging perennial cereal) and in wheat and barley under intermittent freezing stress and under nonfreezing conditions. Activity of glutathione peroxidase (GPX) and four other antioxidative enzymes was also measured under these conditions. DNA repair genes included photolyases involved in repairing ultraviolet‐induced damage and two genes involved in repairing oxidatively induced damage (ERCC1, RAD23). RESULTS Freezing stress was accompanied by large increases in photolyase expression and ERCC1 expression (in wheat and Thinopyrum) and in GPX and GR activity (particularly in Thinopyrum). This is the first report of DNA photolyases being overexpressed under freezing stress. Older Thinopyrum had lower photolyase expression and less freezing‐induced overexpression of ERCC1. Younger Thinopyrum plants sustained more oxidative damage to RNA. CONCLUSIONS Overexpression of DNA repair genes is an important aspect of cold acclimation. When comparing adult cohorts, aging was associated with changes in the freezing stress response, but not with overall increases or decreases in stress tolerance.

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“…is mentioned in the extension literature [5], but the literature includes minimal field research information on the C 4 perennial prairie grasses native to the Prairie Parkland Province of the Great Plains USA. In a greenhouse study, prairie cordgrass (Spartina pectinata), a C 4 perennial prairie grass, was exposed to temperatures as low as −7˚C for up to 3-h and exhibited tolerance to freezing stress [6]. Our objective was to document the damage to field-grown C 4 perennial grasses native to the Great Plains USA associated with a naturally-occurring spring hard freeze.…”

Section: Introductionmentioning

confidence: 99%

Observations of Spring Hard Freeze Injury to C<sub>4</sub> Perennial Grasses Native to the Great Plains, USA

Mitchell¹,

Redfearn²

2019

AJPS

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The native prairies of the Great Plains USA are dominated by perennial C 4 grasses like switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii). Spring hard freeze injury to C 4 perennial grasses is rare but information is lacking in the literature. Our objective was to document effects of spring hard freeze damage to C 4 perennial grasses native to the Great Plains USA. On 2 May at 24:00 pm, air temperature near Mead, Nebraska was below freezing and remained below freezing until 8:00 am on 3 May, with a minimum air temperature of −2.8˚C. Based on 50-year of weather data for this site, a minimum threshold temperature of 0˚C on or after 3 May occurred 16 times, but a minimum threshold temperature of −2.8˚C on or after 3 May occurred only twice. Grass tillers were visually evaluated to determine extent of freeze damage. The terminal 3-to 5-cm of the leaf lamina was blackened 4-d after freezing and had complete browning, rolling, and desiccation 14-d after freezing. Tiller survival was not negatively affected by the freezing temperatures in May 2004. As the growing season progressed, all agronomic and livestock responses were within normal ranges for these C 4 grasses. This is the first field report of multiple C 4 prairie grass species responses to a spring hard freeze following significant spring growth. Plant recovery to this late-spring hard freeze demonstrates the ecological resilience of these C 4 prairie grasses. These rare spring hard freezes had short-term impacts on C 4 grasses but did not negatively impact agronomic performance for forage or bioenergy later in the growing season.

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Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress

Cited by 19 publications

References 85 publications

Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

Nucleic acid damage and DNA repair are affected by freezing stress in annual wheat (Triticum aestivum) and by plant age and freezing in its perennial relative (Thinopyrum intermedium)

Observations of Spring Hard Freeze Injury to C<sub>4</sub> Perennial Grasses Native to the Great Plains, USA

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Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress

Cited by 19 publications

References 85 publications

Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

Nucleic acid damage and DNA repair are affected by freezing stress in annual wheat (Triticum aestivum) and by plant age and freezing in its perennial relative (Thinopyrum intermedium)

Observations of Spring Hard Freeze Injury to C&lt;sub&gt;4&lt;/sub&gt; Perennial Grasses Native to the Great Plains, USA

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Observations of Spring Hard Freeze Injury to C<sub>4</sub> Perennial Grasses Native to the Great Plains, USA