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Citation for Study 16068

Citation title: "Duplicate Gene Divergence by Changes in MicroRNA Binding Sites in Arabidopsis and Brassica".

Study name: "Duplicate Gene Divergence by Changes in MicroRNA Binding Sites in Arabidopsis and Brassica".

This study is part of submission 16068 (Status: Published).

Citation

Wang S., & Adams K.L. 2015. Duplicate Gene Divergence by Changes in MicroRNA Binding Sites in Arabidopsis and Brassica. Genome Biology and Evolution, 7(10).

Authors

• Wang S. (submitter) +17783199905
• Adams K.L.

Abstract

Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes.

Keywords

gene duplication, whole genome duplication, duplicate gene divergence, microRNAs, microRNA binding sites

External links

• DOI: 10.1093/gbe/evv023
• PMID: 25644246
• Other URL: http://gbe.oxfordjournals.org/content/7/3/646

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16068
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref23416,
  	 author = {Sishuo  Wang and Keith Lee Adams},
  	 title = {Duplicate Gene Divergence by Changes in MicroRNA Binding Sites in Arabidopsis and Brassica},
  	 year = {2015},
  	 keywords = {gene duplication, whole genome duplication, duplicate gene divergence, microRNAs, microRNA binding sites},
  	 doi = {10.1093/gbe/evv023},
  	 url = {http://gbe.oxfordjournals.org/content/7/3/646},
  	 pmid = {25644246},
  	 journal = {Genome Biology and Evolution},
  	 volume = {7},
  	 number = {10},
  	 pages = {},
  	 abstract = {Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 23416
  AU  - Wang,Sishuo 
  AU  - Adams,Keith Lee
  T1  - Duplicate Gene Divergence by Changes in MicroRNA Binding Sites in Arabidopsis and Brassica
  PY  - 2015
  KW  - gene duplication
  KW  - whole genome duplication
  KW  - duplicate gene divergence
  KW  - microRNAs
  KW  - microRNA binding sites
  UR  - http://gbe.oxfordjournals.org/content/7/3/646
  N2  - Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes.
  L3  - 10.1093/gbe/evv023
  JF  - Genome Biology and Evolution
  VL  - 7
  IS  - 10
  ER  -