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Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads

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What this work says

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

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Exogenous salicylic acid enhances wheat drought tolerance by influence on the expression of genes related to ascorbate-glutathione cycle

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A small plant-specific protein family of ABI five binding proteins (AFPs) regulates stress response in germinating Arabidopsis seeds and seedlings

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COVAIN: a toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data

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LEA proteins in higher plants: Structure, function, gene expression and regulation

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Chemical analyses of organic residues in archaeological pottery from Arbon Bleiche 3, Switzerland – evidence for dairying in the late Neolithic

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CMA33/XCT Regulates Small RNA Production through Modulating the Transcription of Dicer-Like Genes in Arabidopsis

inferredcites →https://doi.org/10.1016/j.tplants.2014.01.006openalex-snapshot

Engineering crassulacean acid metabolism to improve water-use efficiency

inferredcites →https://doi.org/10.1016/j.ympev.2013.10.010openalex-snapshot

Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae

inferredcites →https://doi.org/10.1017/s0960428602240159openalex-snapshot

Bromeliaceae: Profile of an Adaptive Radiation. D. H. Benzing. Cambridge University Press. 2000. 690pp. ISBN 0 521 43031 3. £80.00 (hardback). DOI: 10.10M/S0960428602240159

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Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

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Widespread adaptive evolution during repeated evolutionary radiations in New World lupins

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The pineapple genome and the evolution of CAM photosynthesis

inferredcites →https://doi.org/10.1038/ng.3617openalex-snapshot

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1046/j.1469-8137.2003.00683.xopenalex-snapshot

Metabolite gradients and carbohydrate translocation in rosette leaves of CAM and C3 bromeliads

inferredcites →https://doi.org/10.1071/fp10084openalex-snapshot

Evolution along the crassulacean acid metabolism continuum

inferredcites →https://doi.org/10.1073/pnas.0303415101openalex-snapshot

Differential metabolic networks unravel the effects of silent plant phenotypes

inferredcites →https://doi.org/10.1073/pnas.0400366101openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1522840113openalex-snapshot

ABA receptor PYL9 promotes drought resistance and leaf senescence

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

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Detecting the Geographical Pattern of Speciation from Species‐Level Phylogenies

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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

inferredcites →https://doi.org/10.1093/bioinformatics/19.2.301openalex-snapshot

r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot

The variant call format and VCFtools

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot

HTSeq—a Python framework to work with high-throughput sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

inferredcites →https://doi.org/10.1093/bioinformatics/btv300openalex-snapshot

GOplot: an R package for visually combining expression data with functional analysis

inferredcites →https://doi.org/10.1093/jexbot/53.369.569openalex-snapshot

Crassulacean acid metabolism: plastic, fantastic

inferredcites →https://doi.org/10.1093/molbev/msi237openalex-snapshot

Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level

inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot

Application of Phylogenetic Networks in Evolutionary Studies

inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot

PAML 4: Phylogenetic Analysis by Maximum Likelihood

inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot

Bayesian Inference of Species Trees from Multilocus Data

inferredcites →https://doi.org/10.1093/molbev/msr311openalex-snapshot

An Improved Likelihood Ratio Test for Detecting Site-Specific Functional Divergence among Clades of Protein-Coding Genes

inferredcites →https://doi.org/10.1093/molbev/mst100openalex-snapshot

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

inferredcites →https://doi.org/10.1093/molbev/msw238openalex-snapshot

Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution

inferredcites →https://doi.org/10.1093/molbev/msx269openalex-snapshot

Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis

inferredcites →https://doi.org/10.1093/nar/30.7.1575openalex-snapshot

An efficient algorithm for large-scale detection of protein families

inferredcites →https://doi.org/10.1093/nar/gks042openalex-snapshot

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

inferredcites →https://doi.org/10.1104/pp.002915openalex-snapshot

How Closely Do the δ13C Values of Crassulacean Acid Metabolism Plants Reflect the Proportion of CO2 Fixed during Day and Night?

inferredcites →https://doi.org/10.1104/pp.110.164277openalex-snapshot

XAP5 CIRCADIAN TIMEKEEPER Regulates Ethylene Responses in Aerial Tissues of Arabidopsis

inferredcites →https://doi.org/10.1104/pp.17.00195openalex-snapshot

On the Evolutionary Origin of CAM Photosynthesis

inferredcites →https://doi.org/10.1105/tpc.107.056655openalex-snapshot

XAP5 CIRCADIAN TIMEKEEPERCoordinates Light Signals for Proper Timing of Photomorphogenesis and the Circadian Clock inArabidopsis

inferredcites →https://doi.org/10.1111/1755-0998.12945openalex-snapshot

A dedicated target capture approach reveals variable genetic markers across micro‐ and macro‐evolutionary time scales in palms

inferredcites →https://doi.org/10.1111/boj.12211openalex-snapshot

Chromosome numbers and DNA content in Bromeliaceae: additional data and critical review

inferredcites →https://doi.org/10.1111/boj.12275openalex-snapshot

Photosynthetic pathways in Bromeliaceae: phylogenetic and ecological significance of CAM and C 3 based on carbon isotope ratios for 1893 species

inferredcites →https://doi.org/10.1111/boj.12423openalex-snapshot

Think tank: water relations of Bromeliaceae in their evolutionary context

inferredcites →https://doi.org/10.1111/j.1365-313x.2006.02889.xopenalex-snapshot

Arabidopsis heat shock transcription factor A2 as a key regulator in response to several types of environmental stress

inferredcites →https://doi.org/10.1111/j.1461-0248.2009.01314.xopenalex-snapshot

The merging of community ecology and phylogenetic biology

inferredcites →https://doi.org/10.1111/j.1461-0248.2010.01530.xopenalex-snapshot

Accelerated rates of climatic‐niche evolution underlie rapid species diversification

inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

inferredcites →https://doi.org/10.1111/nph.13446openalex-snapshot

Crassulacean acid metabolism: a continuous or discrete trait?

inferredcites →https://doi.org/10.1111/pce.12418openalex-snapshot

Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of A rabidopsis thaliana to drought

inferredcites →https://doi.org/10.1111/tpj.13630openalex-snapshot

Temporal and spatial transcriptomic and micro RNA dynamics of CAM photosynthesis in pineapple

inferredcites →https://doi.org/10.1139/cjb-2016-0250openalex-snapshot

Geographic structure in two highly diverse lineages of Tillandsia (Bromeliaceae)

inferredcites →https://doi.org/10.1155/2008/619832openalex-snapshot

Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics

inferredcites →https://doi.org/10.11646/phytotaxa.279.1.1openalex-snapshot

Taxonomic revision of Bromeliaceae subfam. Tillandsioideae based on a multi-locus DNA sequence phylogeny and morphology

inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1371/journal.pbio.1002379openalex-snapshot

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

inferredcites →https://doi.org/10.1371/journal.pcbi.1004873openalex-snapshot

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

inferredcites →https://doi.org/10.1371/journal.pone.0026314openalex-snapshot

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

inferredcites →https://doi.org/10.3732/ajb.92.2.337openalex-snapshot

Phylogenetic relationships in subfamily Tillandsioideae (Bromeliaceae) based on DNA sequence data from seven plastid regions

inferredcites →https://doi.org/10.4161/psb.4.3.7813openalex-snapshot

Drought adaptation in plants with crassulacean acid metabolism involves the flexible use of different storage carbohydrate pools

What points at this work

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

inferred← citeshttps://doi.org/10.1093/botlinnean/boz102openalex-snapshot

Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences

inferred← citeshttps://doi.org/10.12688/f1000research.21779.1openalex-snapshot

A role for MIR828 in pineapple fruit development

inferred← citeshttps://doi.org/10.12688/f1000research.21779.2openalex-snapshot

A role for MIR828 in pineapple fruit development

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