Impact of Whole-Genome and Tandem Duplications in the Expansion and Functional Diversification of the F-Box Family in Legumes (Fabaceae)

F-box proteins constitute a large gene family that regulates processes from hormone signaling to stress response. F-box proteins are the substrate recognition modules of SCF E3 ubiquitin ligases. Here we report very distinct trends in family size, duplication, synteny and transcription of F-box genes in two nitrogen-fixing legumes, Glycine max (soybean) and Medicago truncatula (alfafa). While the soybean FBX genes emerged mainly through segmental duplications (including whole-genome duplications), M. truncatula genome is dominated by locally-duplicated (tandem) F-box genes. Many of these young FBX genes evolved complex transcriptional patterns, including preferential transcription in different tissues, suggesting that they have probably been recruited to important biochemical pathways (e.g. nodulation and seed development).

• Publication year

  2013

• Venue

  PLoS ONE

• Publication date

  2013-02-04

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1371/journal.pone.0055127PMID 23390519PMCID 3563651
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Evolutionary and Biochemical Aspects of Chemical Stress Resistance in Saccharomyces cerevisiae

  2012cited by this paper
• Genome-enabled insights into legume biology.

  2012cited by this paper
• The Expanding Universe of Ubiquitin and Ubiquitin-Like Modifiers1

  2012cited by this paper
• The natural history of ubiquitin and ubiquitin-related domains.

  2012cited by this paper
• Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift

  2011influential reference
• The Pfam protein families database

  2011cited by this paper
• Accelerated Profile HMM Searches

  2011cited by this paper
• Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system.

  2011cited by this paper
• The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

  2011cited by this paper
• Genome sequence of the palaeopolyploid soybean

  2010cited by this paper
• RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

  2010influential reference
• Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory interactions.

  2010cited by this paper
• An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants.

  2010cited by this paper
• Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification

  2009cited by this paper
• Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions

  2009cited by this paper
• Apprehending multicellularity: regulatory networks, genomics, and evolution.

  2009cited by this paper
• Natural history of the E1‐like superfamily: Implication for adenylation, sulfur transfer, and ubiquitin conjugation

  2009cited by this paper
• Circos: an information aesthetic for comparative genomics.

  2009cited by this paper
• Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition.

  2009cited by this paper
• The role of hybridization in plant speciation.

  2009cited by this paper
• A gene expression atlas of the model legume Medicago truncatula.

  2008influential reference
• Turning a hobby into a job: How duplicated genes find new functions

  2008cited by this paper
• Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation.

  2008cited by this paper
• Plant hormones and signaling: common themes and new developments.

  2008cited by this paper
• The Arabidopsis Information Resource (TAIR): gene structure and function annotation

  2007cited by this paper
• The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

  2007cited by this paper
• The Pfam protein families database

  2007cited by this paper
• Consequences of genome duplication.

  2007cited by this paper
• 9) TM4 Microarray Software Suite

  2006cited by this paper
• TM4 microarray software suite.

  2006cited by this paper
• Modification of proteins by ubiquitin and ubiquitin-like proteins.

  2006cited by this paper
• MicroRNAS and their regulatory roles in plants.

  2006cited by this paper
• F-box proteins everywhere.

  2006cited by this paper
• The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains

  2006cited by this paper
• Novel Predicted Peptidases with a Potential Role in the Ubiquitin Signaling Pathway

  2004cited by this paper
• DAGchainer: a tool for mining segmental genome duplications and synteny

  2004influential reference
• Dosage sensitivity and the evolution of gene families in yeast

  2003cited by this paper
• The role of lineage-specific gene family expansion in the evolution of eukaryotes.

  2002cited by this paper
• Plant Development: Regulation by Protein Degradation

  2002cited by this paper
• Evolution and function of ubiquitin-like protein-conjugation systems

  2000cited by this paper
• The ubiquitin system.

  1998cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper

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• Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

  2020cites this paper
• Evolutionary Analysis of the F-Box Gene Family in Saccharomycetaceae

  2019cites this paper
• Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

  2019cites this paper
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  2018cites this paper
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  2018cites this paper
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  2018cites this paper
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  2018cites this paper
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  2017cites this paper
• Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress

  2017influential citation
• Overexpression of MtWRKY76 increases both salt and drought tolerance in Medicago truncatula

  2016cites this paper
• F-box genes: Genome-wide expansion, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri).

  2016cites this paper
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  2016cites this paper
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  2015cites this paper
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  2015cites this paper
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  2015cites this paper
• PTGBase: an integrated database to study tandem duplicated genes in plants

  2015cites this paper
• Plant F-box Proteins – Judges between Life and Death

  2015cites this paper
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  2014cites this paper
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  2014cites this paper
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