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Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae)

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ajb2.1017openalex-snapshot
Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism
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Molecular evolution of key metabolic genes during transitions to C4 and CAM photosynthesis
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Circadian Regulation of Pineapple CAM Photosynthesis
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Ecophysiology of Yucca brevifolia, an arborescent monocot of the Mojave sesert
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Specific Downregulation of the Bacterial-Type PEPC Gene by Artificial MicroRNA Improves Salt Tolerance in Arabidopsis
inferredcites →https://doi.org/10.1016/j.cub.2007.06.036openalex-snapshot
C4 Photosynthesis Evolved in Grasses via Parallel Adaptive Genetic Changes
inferredcites →https://doi.org/10.1016/j.ympev.2015.10.007openalex-snapshot
Evolutionary history of PEPC genes in green plants: Implications for the evolution of CAM in orchids
inferredcites →https://doi.org/10.1016/j.ympev.2016.08.018openalex-snapshot
Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)
inferredcites →https://doi.org/10.1038/nature08747openalex-snapshot
Genome sequencing and analysis of the model grass Brachypodium distachyon
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The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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Reference genome sequence of the model plant Setaria
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Near-optimal probabilistic RNA-seq quantification
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The pineapple genome and the evolution of CAM photosynthesis
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Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nplants.2016.178openalex-snapshot
Transcript, protein and metabolite temporal dynamics in the CAM plant Agave
inferredcites →https://doi.org/10.1038/s41467-017-01064-8openalex-snapshot
The asparagus genome sheds light on the origin and evolution of a young Y chromosome
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The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism
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Underwater CAM photosynthesis elucidated by Isoetes genome
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Chromosome evolution and the genetic basis of agronomically important traits in greater yam
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The genetics of convergent evolution: insights from plant photosynthesis
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The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs
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Bacterial-type Phosphoenolpyruvate Carboxylase (PEPC) Functions as a Catalytic and Regulatory Subunit of the Novel Class-2 PEPC Complex of Vascular Plants
inferredcites →https://doi.org/10.1093/aob/mcaa036openalex-snapshot
Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species, Yucca gloriosa
inferredcites →https://doi.org/10.1093/bioinformatics/bti789openalex-snapshot
Detecting periodic patterns in unevenly spaced gene expression time series using Lomb–Scargle periodograms
inferredcites →https://doi.org/10.1093/bioinformatics/btl056openalex-snapshot
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu333openalex-snapshot
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
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MetaCycle: an integrated R package to evaluate periodicity in large scale data
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UpSetR: an R package for the visualization of intersecting sets and their properties
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Evolutionary Insights on C4 Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics
inferredcites →https://doi.org/10.1093/gbe/evt168openalex-snapshot
Parallel Recruitment of Multiple Genes into C4 Photosynthesis
inferredcites →https://doi.org/10.1093/jxb/ern008openalex-snapshot
Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)
inferredcites →https://doi.org/10.1093/jxb/eru053openalex-snapshot
Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)
inferredcites →https://doi.org/10.1093/jxb/eru087openalex-snapshot
Shared origins of a key enzyme during the evolution of C4 and CAM metabolism
inferredcites →https://doi.org/10.1093/jxb/eru100openalex-snapshot
Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species
inferredcites →https://doi.org/10.1093/jxb/eru185openalex-snapshot
Light quality modulates metabolic synchronization over the diel phases of crassulacean acid metabolism
inferredcites →https://doi.org/10.1093/jxb/eru234openalex-snapshot
Multiple isoforms of phosphoenolpyruvate carboxylase in the Orchidaceae (subtribe Oncidiinae): implications for the evolution of crassulacean acid metabolism
inferredcites →https://doi.org/10.1093/jxb/erv536openalex-snapshot
Gas exchange and leaf anatomy of a C3–CAM hybrid,Yucca gloriosa(Asparagaceae)
inferredcites →https://doi.org/10.1093/jxb/erz105openalex-snapshot
Shared expression of crassulacean acid metabolism (CAM) genes pre-dates the origin of CAM in the genus Yucca
inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/nar/gkl315openalex-snapshot
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
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The TIGR Rice Genome Annotation Resource: improvements and new features
inferredcites →https://doi.org/10.1093/nar/gkr944openalex-snapshot
Phytozome: a comparative platform for green plant genomics
inferredcites →https://doi.org/10.1104/pp.111.179275openalex-snapshot
Conserved and Divergent Rhythms of Crassulacean Acid Metabolism-Related and Core Clock Gene Expression in the Cactus Opuntia ficus-indica
inferredcites →https://doi.org/10.1104/pp.123.4.1471openalex-snapshot
A Minimal Serine/Threonine Protein Kinase Circadianly Regulates Phospho enol pyruvate Carboxylase Activity in Crassulacean Acid Metabolism-Induced Leaves of the Common Ice Plant
inferredcites →https://doi.org/10.1104/pp.15.01076openalex-snapshot
Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare
inferredcites →https://doi.org/10.1105/tpc.17.00301openalex-snapshot
Phosphorylation of Phospho enol pyruvate Carboxylase Is Essential for Maximal and Sustained Dark CO 2 Fixation and Core Circadian Clock Operation in the Obligate Crassulacean Acid Metabolism Species Kalanchoë fedtschenkoi
inferredcites →https://doi.org/10.1105/tpc.19.00481openalex-snapshot
Kalanchoë PPC1 Is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03274.xopenalex-snapshot
Bacterial‐ and plant‐type phosphoenolpyruvate carboxylase polypeptides interact in the hetero‐oligomeric Class‐2 PEPC complex of developing castor oil seeds
inferredcites →https://doi.org/10.1111/j.1469-8137.2009.02929.xopenalex-snapshot
Genetic changes contributing to the parallel evolution of red floral pigmentation among Ipomoea species
inferredcites →https://doi.org/10.1111/nph.13446openalex-snapshot
Crassulacean acid metabolism: a continuous or discrete trait?
inferredcites →https://doi.org/10.1111/nph.15851openalex-snapshot
Evolutionary trajectories, accessibility and other metaphors: the case of C4 and CAM photosynthesis
inferredcites →https://doi.org/10.1111/nph.16089openalex-snapshot
Evolution of l ‐ DOPA 4,5‐dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales
inferredcites →https://doi.org/10.1111/tpj.13415openalex-snapshot
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
inferredcites →https://doi.org/10.1111/tpj.13781openalex-snapshot
The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization
inferredcites →https://doi.org/10.1126/science.1241089openalex-snapshot
The Amborella Genome and the Evolution of Flowering Plants
inferredcites →https://doi.org/10.1126/science.1255274openalex-snapshot
The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
inferredcites →https://doi.org/10.1130/g33147.1openalex-snapshot
Neogene aridification of the Northern Hemisphere
inferredcites →https://doi.org/10.1177/0748730410379711openalex-snapshot
JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets
inferredcites →https://doi.org/10.1186/1471-2229-10-200openalex-snapshot
Characterization of bacterial-type phosphoenolpyruvate carboxylase expressed in male gametophyte of higher plants
inferredcites →https://doi.org/10.1186/gb-2008-9-8-r130openalex-snapshot
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development
inferredcites →https://doi.org/10.1186/s12864-018-4964-7openalex-snapshot
Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave
inferredcites →https://doi.org/10.1186/s12864-020-06824-3openalex-snapshot
Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs
inferredcites →https://doi.org/10.1186/s13059-019-1832-yopenalex-snapshot
OrthoFinder: phylogenetic orthology inference for comparative genomics
inferredcites →https://doi.org/10.1371/journal.pgen.0040014openalex-snapshot
Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
inferredcites →https://doi.org/10.1371/journal.pgen.1004365openalex-snapshot
Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis
inferredcites →https://doi.org/10.1371/journal.pgen.1008209openalex-snapshot
Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album
inferredcites →https://doi.org/10.1371/journal.pone.0012887openalex-snapshot
Maize Global Transcriptomics Reveals Pervasive Leaf Diurnal Rhythms but Rhythms in Developing Ears Are Largely Limited to the Core Oscillator
inferredcites →https://doi.org/10.1371/journal.pone.0016907openalex-snapshot
Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules
inferredcites →https://doi.org/10.1534/genetics.104.031153openalex-snapshot
Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3389/fpls.2018.01757openalex-snapshot
Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C3 Photosynthesis Plant Arabidopsis thaliana
inferredcites →https://doi.org/10.3389/fpls.2018.02000openalex-snapshot
Altered Gene Regulatory Networks Are Associated With the Transition From C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)
inferredcites →https://doi.org/10.3732/ajb.1600198openalex-snapshot
Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae)
inferredcites →https://doi.org/10.7717/peerj.7755openalex-snapshot
Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1002/aps3.70071openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.semcdb.2023.07.013openalex-snapshot
The Calvin-Benson-Bassham cycle in C4 and Crassulacean acid metabolism species
inferred← citeshttps://doi.org/10.1016/j.xplc.2023.100772openalex-snapshot
Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate
inferred← citeshttps://doi.org/10.1093/aob/mcad039openalex-snapshot
Forty years of research into crassulacean acid metabolism in the genus Clusia : anatomy, ecophysiology and evolution
inferred← citeshttps://doi.org/10.1093/aob/mcad062openalex-snapshot
The Agavoideae: an emergent model clade for CAM evolutionary biology
inferred← citeshttps://doi.org/10.1093/aob/mcad135openalex-snapshot
The CAM lineages of planet Earth
inferred← citeshttps://doi.org/10.1093/jxb/erag234openalex-snapshot
Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca
inferred← citeshttps://doi.org/10.1093/plcell/koae130openalex-snapshot
CAM evolution is associated with gene family expansion in an explosive bromeliad radiation
inferred← citeshttps://doi.org/10.1093/plphys/kiac303openalex-snapshot
Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future
inferred← citeshttps://doi.org/10.1093/plphys/kiaf095openalex-snapshot
Regulation of Crassulacean acid metabolism at the protein level in Kalanchoë laxiflora
inferred← citeshttps://doi.org/10.1101/2023.04.20.537669openalex-snapshot
The genome of Talinum fruticosum
inferred← citeshttps://doi.org/10.1101/2024.11.06.622337openalex-snapshot
A high-quality genome of the mass-blooming desert plant Cistanthe longiscapa and its photosynthetic behavior related to drought and life history
inferred← citeshttps://doi.org/10.1101/2025.09.24.677520openalex-snapshot
Techniques and challenges in studying photosynthetic diversity in freshwater aquatic vascular plants
inferred← citeshttps://doi.org/10.1111/mec.70313openalex-snapshot
Divergent Transcriptional Architectures Beyond Core CAM Genes in Facultative and Constitutive CAM Species in Tillandsia L.
inferred← citeshttps://doi.org/10.1111/nph.70186openalex-snapshot
A high‐quality genome of the Atacama Desert plant Cistanthe cachinalensis and its photosynthetic behavior related to drought and life history
inferred← citeshttps://doi.org/10.1111/nph.70437openalex-snapshot
Cryptic CAM photosynthesis in Joshua tree ( Yucca brevifolia , Y. jaegeriana )
inferred← citeshttps://doi.org/10.1186/s12870-023-04186-yopenalex-snapshot
The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.21203/rs.3.rs-10909807/v1openalex-snapshot
Transcriptomics of C 3 +CAM Peperomia species reveals potential initial steps toward a CAM pathway
inferred← citeshttps://doi.org/10.3389/fpls.2024.1397058openalex-snapshot
Deciphering the maize gene ZmGF14–3: implications for plant height based on co-expression networks
inferred← citeshttps://doi.org/10.3390/horticulturae9030398openalex-snapshot
Mechanisms Underlying the C3–CAM Photosynthetic Shift in Facultative CAM Plants
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626116openalex-snapshot
Additional file 1 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626119openalex-snapshot
Additional file 2 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626122openalex-snapshot
Additional file 3 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626125openalex-snapshot
Additional file 4 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626128openalex-snapshot
Additional file 5 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626131openalex-snapshot
Additional file 6 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626134openalex-snapshot
Additional file 7 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
inferred← citeshttps://doi.org/10.6084/m9.figshare.22626137openalex-snapshot
Additional file 8 of The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways
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