Altered Gene Regulatory Networks Are Associated With the Transition From C to Crassulacean Acid Metabolism in (Oncidiinae: Orchidaceae) (Q61808063)

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English	Altered Gene Regulatory Networks Are Associated With the Transition From C to Crassulacean Acid Metabolism in (Oncidiinae: Orchidaceae)	article

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scholarly article

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Altered Gene Regulatory Networks Are Associated With the Transition From C to Crassulacean Acid Metabolism in (Oncidiinae: Orchidaceae) (English)

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transcriptomics

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1 reference

based on heuristic

inferred from title

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Jim Leebens-Mack

10

object named as

Jim Leebens-Mack

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9

object named as

Klaus Winter

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Karolina Heyduk

1

object named as

Karolina Heyduk

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author name string

Michelle Hwang

2

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Victor Albert

3

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Katia Silvera

4

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Tianying Lan

5

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Kimberly Farr

6

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Tien-Hao Chang

7

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Ming-Tsair Chan

8

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publication date

2018

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Frontiers in Plant Science

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9

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2000

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copyright license

Creative Commons Attribution 4.0 International

28 January 2019

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April 2022 Public Data File from Crossref

copyright status

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describes a project that uses

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Cytoscape

2 references

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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Purification of the phosphorylated night form and dephosphorylated day form of phosphoenolpyruvate carboxylase from Bryophyllum fedtschenkoi

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Differential Patterns of Expression of the Arabidopsis PHYB, PHYD, and PHYE Phytochrome Genes

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Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light

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Metabolite Control Overrides Circadian Regulation of Phosphoenolpyruvate Carboxylase Kinase and CO(2) Fixation in Crassulacean Acid Metabolism

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The regulation of phosphoenolpyruvate carboxylase in CAM plants

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Role of malate synthesis mediated by phosphoenolpyruvate carboxylase in guard cells in the regulation of stomatal movement.

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ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis

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A minimal serine/threonine protein kinase circadianly regulates phosphoenolpyruvate carboxylase activity in crassulacean acid metabolism-induced leaves of the common ice plant

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Functional interaction of phytochrome B and cryptochrome 2.

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New partial sequences of phosphoenolpyruvate carboxylase as molecular phylogenetic markers

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Molecular Genetics of Crassulacean Acid Metabolism

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A phytochrome-associated protein phosphatase 2A modulates light signals in flowering time control in Arabidopsis

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Integrating diel starch metabolism with the circadian and environmental regulation of Crassulacean acid metabolism in Mesembryanthemum crystallinum

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The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks.

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

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Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana

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12 December 2020

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Multiple origins of crassulacean acid metabolism and the epiphytic habit in the Neotropical family Bromeliaceae

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https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

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CRASSULACEAN ACID METABOLISM: Molecular Genetics.

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https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Roots, cycles and leaves. Expression of the phosphoenolpyruvate carboxylase kinase gene family in soybean

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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Epiphytism and pollinator specialization: drivers for orchid diversity?

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

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Conservation and divergence of circadian clock operation in a stress-inducible Crassulacean acid metabolism species reveals clock compensation against stress

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The co-ordination of central plant metabolism by the circadian clock

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maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments

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https://pubmed.ncbi.nlm.nih.gov/30745906

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Dark Fixation of CO(2) by Tobacco Leaves

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Osmoregulation in Cotton Fiber: Accumulation of Potassium and Malate during Growth

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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Relationships between Stomatal Behavior and Internal Carbon Dioxide Concentration in Crassulacean Acid Metabolism Plants.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Seasonal Shifts of Photosynthesis in Portulacaria afra (L.) Jacq

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

inferred from PubMed ID database lookup

Characterization and functional analysis of phosphoenolpyruvate carboxylase kinase genes in rice

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

TIME FOR COFFEE encodes a nuclear regulator in the Arabidopsis thaliana circadian clock

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Arabidopsis vacuolar malate channel is a member of the ALMT family.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mfuzz: a software package for soft clustering of microarray data

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https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Functional constraints of CAM leaf anatomy: tight cell packing is associated with increased CAM function across a gradient of CAM expression

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

inferred from PubMed ID database lookup

Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM).

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

inferred from PubMed ID database lookup

Higher plants use LOV to perceive blue light.

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based on heuristic

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Crassulacean acid metabolism and epiphytism linked to adaptive radiations in the Orchidaceae

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https://pubmed.ncbi.nlm.nih.gov/30745906

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inferred from PubMed ID database lookup

The Arabidopsis rcn1-1 mutation impairs dephosphorylation of Phot2, resulting in enhanced blue light responses

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https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

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The role of proteins in C(3) plants prior to their recruitment into the C(4) pathway

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

inferred from PubMed ID database lookup

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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inferred from PubMed ID database lookup

LOV domain-containing F-box proteins: light-dependent protein degradation modules in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

inferred from PubMed ID database lookup

Arabidopsis PYR/PYL/RCAR receptors play a major role in quantitative regulation of stomatal aperture and transcriptional response to abscisic acid.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

inferred from PubMed ID database lookup

PYR/RCAR receptors contribute to ozone-, reduced air humidity-, darkness-, and CO2-induced stomatal regulation.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Arabidopsis PPP family of serine/threonine protein phosphatases: many targets but few engines.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

TIME FOR COFFEE is an essential component in the maintenance of metabolic homeostasis in Arabidopsis thaliana

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Leaf anatomical traits which accommodate the facultative engagement of crassulacean acid metabolism in tropical trees of the genus Clusia.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Shared origins of a key enzyme during the evolution of C4 and CAM metabolism

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

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Trimmomatic: a flexible trimmer for Illumina sequence data

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

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based on heuristic

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Light quality modulates metabolic synchronization over the diel phases of crassulacean acid metabolism

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

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Multiple isoforms of phosphoenolpyruvate carboxylase in the Orchidaceae (subtribe Oncidiinae): implications for the evolution of crassulacean acid metabolism

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

AliView: a fast and lightweight alignment viewer and editor for large datasets

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https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The single-subunit RING-type E3 ubiquitin ligase RSL1 targets PYL4 and PYR1 ABA receptors in plasma membrane to modulate abscisic acid signaling

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Tobacco guard cells fix CO2 by both Rubisco and PEPcase while sucrose acts as a substrate during light-induced stomatal opening

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crassulacean acid metabolism: a continuous or discrete trait?

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The pineapple genome and the evolution of CAM photosynthesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Near-optimal probabilistic RNA-seq quantification

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Orchestration of carbohydrate processing for crassulacean acid metabolism.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Integration of omic networks in a developmental atlas of maize.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae).

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcript, protein and metabolite temporal dynamics in the CAM plant Agave

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

On the Evolutionary Origin of CAM Photosynthesis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Network propagation in the cytoscape cyberinfrastructure.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales).

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

1 reference

https://pubmed.ncbi.nlm.nih.gov/30745906

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.3389/FPLS.2018.02000

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