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Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications may have facilitated adaptation to different environmental conditions

https://doi.org/10.1101/585232
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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/jez.b.22598openalex-snapshot
Phylogenomics reveals surprising sets of essential and dispensable clades of MIKCc‐group MADS‐box genes in flowering plants
inferredcites →https://doi.org/10.1007/s00122-016-2727-xopenalex-snapshot
Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat
inferredcites →https://doi.org/10.1007/s00425-005-0123-xopenalex-snapshot
Overexpression of TaMADS1, a SEPALLATA-like gene in wheat, causes early flowering and the abnormal development of floral organs in Arabidopsis
inferredcites →https://doi.org/10.1007/s00438-014-0912-7openalex-snapshot
Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage)
inferredcites →https://doi.org/10.1007/s00497-002-0158-0openalex-snapshot
WAG, a wheat AGAMOUS homolog, is associated with development of pistil-like stamens in alloplasmic wheats
inferredcites →https://doi.org/10.1007/s11103-004-0416-7openalex-snapshot
Defining subdomains of the K domain important for protein?protein interactions of plant MADS proteins
inferredcites →https://doi.org/10.1007/s11103-009-9504-zopenalex-snapshot
Class D and Bsister MADS-box genes are associated with ectopic ovule formation in the pistil-like stamens of alloplasmic wheat (Triticum aestivum L.)
inferredcites →https://doi.org/10.1007/s12571-011-0140-5openalex-snapshot
Crops that feed the world 6. Past successes and future challenges to the role played by maize in global food security
inferredcites →https://doi.org/10.1007/s12571-013-0263-yopenalex-snapshot
Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security
inferredcites →https://doi.org/10.1016/j.crvi.2016.05.005openalex-snapshot
Superheroes and masterminds of plant domestication
inferredcites →https://doi.org/10.1016/j.gene.2004.12.014openalex-snapshot
MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants
inferredcites →https://doi.org/10.1016/j.gep.2013.02.004openalex-snapshot
Analysis of the expression of the AGL17-like clade of MADS-box transcription factors in rice
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Transposons: a blessing curse
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Genome-wide analysis of the MADS-box gene family in polyploid cotton (Gossypium hirsutum) and in its diploid parental species (Gossypium arboreum and Gossypium raimondii)
inferredcites →https://doi.org/10.1016/j.semcdb.2009.10.004openalex-snapshot
The ‘ABC’ of MADS domain protein behaviour and interactions
inferredcites →https://doi.org/10.1016/j.tig.2005.02.010openalex-snapshot
Dosage balance in gene regulation: biological implications
inferredcites →https://doi.org/10.1016/j.tplants.2018.04.008openalex-snapshot
Array of MADS-Box Genes: Facilitator for Rapid Adaptation?
inferredcites →https://doi.org/10.1016/s1055-7903(03)00207-0openalex-snapshot
The major clades of MADS-box genes and their role in the development and evolution of flowering plants
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Complexes of MADS-box proteins are sufficient to convert leaves into floral organs
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The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14
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ModelFinder: fast model selection for accurate phylogenetic estimates
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Genome-wide analysis of banana MADS-box family closely related to fruit development and ripening
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The SOC1 MADS‐box gene integrates vernalization and gibberellin signals for flowering in Arabidopsis
inferredcites →https://doi.org/10.1071/cp16420openalex-snapshot
Effect of VRN1 and PPD1 genes on anthesis date and wheat growth
inferredcites →https://doi.org/10.1073/pnas.042677699openalex-snapshot
Analysis of MADS box protein–protein interactions in living plant cells
inferredcites →https://doi.org/10.1073/pnas.0937399100openalex-snapshot
Positional cloning of the wheat vernalization gene VRN1
inferredcites →https://doi.org/10.1073/pnas.1635053100openalex-snapshot
MADS box genes control vernalization-induced flowering in cereals
inferredcites →https://doi.org/10.1073/pnas.97.10.5328openalex-snapshot
An ancestral MADS-box gene duplication occurred before the divergence of plants and animals
inferredcites →https://doi.org/10.1080/10408690290825510openalex-snapshot
Wheat Protein Composition and Properties of Wheat Glutenin in Relation to Breadmaking Functionality
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MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
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shinyCircos: an R/Shiny application for interactive creation of Circos plot
inferredcites →https://doi.org/10.1093/jxb/erp058openalex-snapshot
Wheat
inferredcites →https://doi.org/10.1093/jxb/erx479openalex-snapshot
MADS-box genes and crop domestication: the jack of all traits
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/mst024openalex-snapshot
Ultrafast Approximation for Phylogenetic Bootstrap
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot
UFBoot2: Improving the Ultrafast Bootstrap Approximation
inferredcites →https://doi.org/10.1093/nar/24.16.3134openalex-snapshot
DNA-binding properties of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA and AGAMOUS
inferredcites →https://doi.org/10.1093/nar/gkh454openalex-snapshot
CD-Search: protein domain annotations on the fly
inferredcites →https://doi.org/10.1093/nar/gkn900openalex-snapshot
The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in ‘floral quartet’-like complexes in vitro
inferredcites →https://doi.org/10.1093/nar/gkq1189openalex-snapshot
CDD: a Conserved Domain Database for the functional annotation of proteins
inferredcites →https://doi.org/10.1093/nar/gku1221openalex-snapshot
CDD: NCBI's conserved domain database
inferredcites →https://doi.org/10.1093/nar/gkw1129openalex-snapshot
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
inferredcites →https://doi.org/10.1093/nar/gkw419openalex-snapshot
Heatmapper: web-enabled heat mapping for all
inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot
The Pfam protein families database in 2019
inferredcites →https://doi.org/10.1093/pcp/pcg171openalex-snapshot
WAP1, a Wheat APETALA1 Homolog, Plays a Central Role in the Phase Transition from Vegetative to Reproductive Growth
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1098/rstb.2016.0429openalex-snapshot
Geographic mosaics and changing rates of cereal domestication
inferredcites →https://doi.org/10.1101/510388openalex-snapshot
Wheat VRN1 , FUL2 and FUL3 play critical and redundant roles in spikelet development and spike determinacy
inferredcites →https://doi.org/10.1101/gad.1518407openalex-snapshot
Role of SVP in the control of flowering time by ambient temperature in Arabidopsis
inferredcites →https://doi.org/10.1101/gr.177001openalex-snapshot
The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic Analysis
inferredcites →https://doi.org/10.1101/gr.217117.116openalex-snapshot
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
inferredcites →https://doi.org/10.1104/pp.106.089805openalex-snapshot
MIKC* MADS-Protein Complexes Bind Motifs Enriched in the Proximal Region of Late Pollen-Specific Arabidopsis Promoters
inferredcites →https://doi.org/10.1104/pp.15.01667openalex-snapshot
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform
inferredcites →https://doi.org/10.1105/tpc.004127openalex-snapshot
The TRANSPARENT TESTA16 Locus Encodes the ARABIDOPSIS BSISTER MADS Domain Protein and Is Required for Proper Development and Pigmentation of the Seed Coat
inferredcites →https://doi.org/10.1105/tpc.011544openalex-snapshot
Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.019679openalex-snapshot
Ectopic Expression of the Petunia MADS Box Gene UNSHAVEN Accelerates Flowering and Confers Leaf-Like Characteristics to Floral Organs in a Dominant-Negative Manner[W]
inferredcites →https://doi.org/10.1105/tpc.107.050377openalex-snapshot
MicroRNA-Mediated Regulation of Stomatal Development in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.107.051813openalex-snapshot
Genetic and Epigenetic Alteration among Three Homoeologous Genes of a Class E MADS Box Gene in Hexaploid Wheat
inferredcites →https://doi.org/10.1105/tpc.111.094854openalex-snapshot
The MADS29 Transcription Factor Regulates the Degradation of the Nucellus and the Nucellar Projection during Rice Seed Development
inferredcites →https://doi.org/10.1105/tpc.113.110049openalex-snapshot
Functional Conservation of MIKC*-Type MADS Box Genes in Arabidopsis and Rice Pollen Maturation
inferredcites →https://doi.org/10.1105/tpc.114.124685openalex-snapshot
miR824-Regulated AGAMOUS-LIKE16 Contributes to Flowering Time Repression in Arabidopsis
inferredcites →https://doi.org/10.1111/j.1365-313x.2011.04878.xopenalex-snapshot
The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.05069.xopenalex-snapshot
Targeted inactivation of transcription factors by overexpression of their truncated forms in plants
inferredcites →https://doi.org/10.1111/nph.13077openalex-snapshot
The floral transcriptome of E ucalyptus grandis
inferredcites →https://doi.org/10.1111/nph.13533openalex-snapshot
Genomics as the key to unlocking the polyploid potential of wheat
inferredcites →https://doi.org/10.1111/tpj.13055openalex-snapshot
Non‐canonical structure, function and phylogeny of the B sister MADS ‐box gene O s MADS 30 of rice ( O ryza sativa)
inferredcites →https://doi.org/10.1126/science.290.5499.2105openalex-snapshot
Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes
inferredcites →https://doi.org/10.1126/science.aar6089openalex-snapshot
The transcriptional landscape of polyploid wheat
inferredcites →https://doi.org/10.1126/science.aar7191openalex-snapshot
Shifting the limits in wheat research and breeding using a fully annotated reference genome
inferredcites →https://doi.org/10.1186/1471-2164-14-728openalex-snapshot
Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
inferredcites →https://doi.org/10.1186/1471-2164-8-242openalex-snapshot
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress
inferredcites →https://doi.org/10.1186/gb-2004-5-6-226openalex-snapshot
An overview of the basic helix-loop-helix proteins.
inferredcites →https://doi.org/10.1186/gb-2006-7-s1-s10openalex-snapshot
Automatic annotation of eukaryotic genes, pseudogenes and promoters
inferredcites →https://doi.org/10.1186/gb-2009-10-2-r24openalex-snapshot
SEPALLATA3: the 'glue' for MADS box transcription factor complex formation
inferredcites →https://doi.org/10.1186/gb-2010-11-6-214openalex-snapshot
A hitchhiker's guide to the MADS world of plants
inferredcites →https://doi.org/10.1186/s12864-016-2684-4openalex-snapshot
The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression
inferredcites →https://doi.org/10.1186/s12870-015-0511-8openalex-snapshot
Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)
inferredcites →https://doi.org/10.1186/s12870-018-1259-8openalex-snapshot
MADS-box family genes in sheepgrass and their involvement in abiotic stress responses
inferredcites →https://doi.org/10.1186/s13059-015-0601-9openalex-snapshot
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome
inferredcites →https://doi.org/10.1186/s13059-015-0754-6openalex-snapshot
Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B
inferredcites →https://doi.org/10.1186/s13059-018-1491-4openalex-snapshot
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
inferredcites →https://doi.org/10.1242/dev.134080openalex-snapshot
MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution
inferredcites →https://doi.org/10.1242/dev.172965openalex-snapshot
How can developmental biology help feed a growing population?
inferredcites →https://doi.org/10.1371/journal.pgen.1007662openalex-snapshot
Rice transcription factor OsMADS25 modulates root growth and confers salinity tolerance via the ABA–mediated regulatory pathway and ROS scavenging
inferredcites →https://doi.org/10.1371/journal.pone.0051435openalex-snapshot
Live and Let Die - The Bsister MADS-Box Gene OsMADS29 Controls the Degeneration of Cells in Maternal Tissues during Seed Development of Rice (Oryza sativa)
inferredcites →https://doi.org/10.1371/journal.pone.0084781openalex-snapshot
Genome-Wide Analysis of the MADS-Box Gene Family in Brachypodium distachyon
inferredcites →https://doi.org/10.1534/g3.117.043679openalex-snapshot
Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat
inferredcites →https://doi.org/10.3389/fpls.2017.01081openalex-snapshot
Cloning and Functional Analysis of MADS-box Genes, TaAG-A and TaAG-B, from a Wheat K-type Cytoplasmic Male Sterile Line
inferredcites →https://doi.org/10.3389/fpls.2018.01185openalex-snapshot
Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution
inferredcites →https://doi.org/10.3390/biology2031150openalex-snapshot
Phylogenomics of MADS-Box Genes in Plants — Two Opposing Life Styles in One Gene Family
inferredcites →https://doi.org/10.3390/f9060304openalex-snapshot
Genome-Wide Identification and Characterization of MADS-box Family Genes Related to Floral Organ Development and Stress Resistance in Hevea brasiliensis Müll. Arg.

What points at this work

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inferred← citeshttps://doi.org/10.3389/fpls.2021.777494openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/plants12132465openalex-snapshot
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