The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Yang, Xiaohan; Hu, Rongbin; Yin, Hengfu; Jenkins, Jerry; Shu, Shengqiang; Tang, Haibao; Liu, Degao; Weighill, Deborah; Yim, Won Cheol; Ha, Jung Min; Heyduk, Karolina; Goodstein, David; Guo, Hao; Moseley, Robert C.; Fitzek, Elisabeth; Jawdy, Sara; Zhang, Zhihao; Xie, Meng; Hartwell, James; Abraham, Paul E.; Beltrán, Juan D.; Boxall, Susanna Flavia; Dever, Louisa V.; Palla, Kaitlin J.; Albion, Rebecca L.; Garcia, Travis M.; Mayer, Jesse A.; Lim, Sung Don; Wai, Ching Man; Peluso, Paul; Buren, Robert Van; DePaoli, Henrique C.; Borland, Anne M.; Guo, Hong; Chen, Jay; Muchero, Wellington; Yin, Yanbin; Jacobson, Daniel; Tschaplinski, Timothy J.; Hettich, Robert L.; Ming, Ray; Winter, Klaus; Leebens‐Mack, James H.; Smith, J. Andrew C.; Cushman, John C.; Schmutz, Jeremy; Tuskan, Gerald A.

doi:10.1038/s41467-017-01491-7

Cited by 162 publications

(267 citation statements)

References 78 publications

(103 reference statements)

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“…This could be explained by the time-ofday-dependent phosphorylation of the phosphoenolpyruvate carboxylase enzyme that fixes CO 2 into malate at night (Nimmo et al 1987). These early reports would later be supported by data on how this process is regulated by the clock in Kalancho€ e at the transcriptional level Yang et al 2017).…”

Section: The Molecular Clockmentioning

confidence: 81%

On the move through time – a historical review of plant clock research

Johansson

Köster

2018

Plant Biol J

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The circadian clock is an important regulator of growth and development that has evolved to help organisms to anticipate the predictably occurring events on the planet, such as light-dark transitions, and adapt growth and development to these. This review looks back in history on how knowledge about the endogenous biological clock has been acquired over the centuries, with a focus on discoveries in plants. Key findings at the physiological, genetic and molecular level are described and the role of the circadian clock in important molecular processes is reviewed.

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Section: The Molecular Clockmentioning

confidence: 81%

On the move through time – a historical review of plant clock research

Johansson

Köster

2018

Plant Biol J

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“…orthologues of OST1, HT1, PP2C, RCAR3 , K + transporter AKT2/3 , chloride channel CLC‐c , Ca 2+ transporter ACA2 and ECA4 ), stomatal signalling components in pineapple (e.g. orthologues of BLUS1, HT1, CPK6 ), an H 2 O 2 detoxification enzyme (orthologue of CAT2 ) implicated in the stomatal signalling process and a blue‐light receptor ( PHOT2 ) in K. fedtschenkoi (Abraham et al , ; Yang et al , ; Wai and VanBuren, ; Moseley et al , ). Among these genes, only PHOT2 has been shown through a functional study to have a direct implication for CAM stomatal behaviour in K. fedtschenkoi (Liu et al , ).…”

Section: Stomatal Physiology: Sensitivity and Signalling Processes Acmentioning

confidence: 99%

“…Firstly, Kalanchoe genome analysis provided evidence for contrasting differential regulation of carbohydrate processing between CAM and C3 species. A network analysis compared families of carbohydrate ‘active’ gene families which were similar in number to those found in Arabidopsis but with altered expression profiles, with a possible role for a trehalose‐6‐phosphate synthase and an invertase, acting to alter carbohydrate partitioning between substrates for CAM and those needed for growth (Yang et al , ). Secondly, putative orthologues of chloroplast and vacuolar sugar transporters of pineapple have adopted a defined diel expression pattern, and are hence implicated in the diel processing of carbohydrate in this soluble‐sugar‐processing CAM species (Borland et al , ).…”

Section: Modelling Approaches Capture the Complex Control Of Cam Mesomentioning

confidence: 99%

“…The availability of CAM genomes has provided a springboard for analysis of orthologues and shared transcriptional control elements (Ming et al, 2015;Yang et al, 2017;Wai et al, 2019), whereas emerging comparative 'omics' analysis of various CAM species has also contributed to a more in-depth understanding of regulatory networks (Abraham et al, 2016;Chiang et al, 2016;Zhang et al, 2016;Yin et al, 2018;Heyduk et al, 2019). Comparative transcriptomic studies have provided insights into the evolutionary trajectory of CAM and suggest that transcriptional regulation is primarily associated with specific expression profiles of key CAM genes.…”

Section: Introductionmentioning

confidence: 99%

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Model approaches to advance crassulacean acid metabolism system integration

Chomthong

Griffiths

2020

The Plant Journal

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Summary This review summarises recent progress in understanding crassulacean acid metabolism (CAM) systems and the integration of internal and external stimuli to maximise water‐use efficiency. Complex CAM traits have been reduced to their minimum and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large‐scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address the evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water‐use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co‐expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that the resultant improvements of bottom‐up, mechanistic modelling systems can enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.

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“…Beyond the plants themselves, the genes regulating water storage and other succulence‐associated traits, notably CAM and the capacity for carbon sequestration, may become more valuable as a resource than the species from which they are identified. Crop enhancement efforts using CAM engineered into C3 plants are well underway within research programmes considering both succulent and non‐succulent species (Borland et al, ; Yang et al, ). The genetic basis for extreme drought tolerance, likewise, has been the subject of coordinated research efforts focusing on the (non‐succulent) model species Xerophyta viscosa (Velloziaceae), a resurrection plant (Hillhorst & Farrant, ).…”

Section: The Value Of Desert Succulentsmentioning

confidence: 99%

Succulent plant diversity as natural capital

Grace

2019

Plants People Planet

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Societal Impact Statement Drought‐tolerant plants are increasingly recognized as a resource to mitigate the consequences of climate change. Succulent plants use stored water to sustain metabolism during regular droughts; succulence is a highly successful adaptation that has evolved in thousands of species throughout the plant kingdom. Desert (xeromorphic) succulent species are a potentially relevant resource to manage environments and energy supply in the hottest and driest places. However, many species are threatened with extinction or could become invasive outside their natural range. This review highlights research needed to develop desert succulents as a sustainable resource in a carbon economy. Summary Drought and increased temperature of the Earth's surface pose significant social and economic challenges under the anticipated effects of climate change. The presence of a reservoir of water to sustain metabolism under drought conditions is a conceptually simple, but remarkably complex, adaptation in the plant kingdom known broadly as succulence. The trait has arisen repeatedly among flowering plant lineages: thousands of succulent species representing immense taxonomic diversity are found on all continents except the polar regions. The phylogenetic diversity and ecological adaptations of desert‐adapted (xeromorphic) succulent plants could be particularly relevant resources to meet the challenges of environmental change, in applications as varied as bioenergy, urban greening, and high‐value products. However, a more complex picture is emerging in which xeromorphic succulents endemic to arid and semi‐arid regions could be at risk of extinction due to habitat loss and exploitation, while others could become invasive if introduced outside their natural range, thus compounding an existing problem of invasive succulent plant species. This review aims to summarize the state of current knowledge of xeromorphic succulent plants as a resource, draw attention to conservation concerns, and examine the potential for their unique traits to be harnessed in a climate change‐resilient world.

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The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Cited by 162 publications

References 78 publications

On the move through time – a historical review of plant clock research

On the move through time – a historical review of plant clock research

Model approaches to advance crassulacean acid metabolism system integration

Succulent plant diversity as natural capital

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