title: Molecular evolution and diversification of the Argonaute family of proteins in plants.
abstract: BACKGROUND
  Argonaute (AGO) proteins form the core of the RNA-induced silencing complex, a central component of the smRNA machinery. Although reported from several plant species, little is known about their evolution. Moreover, these genes have not yet been cloned from the ecological model plant, Nicotiana attenuata, in which the smRNA machinery is known to mediate important ecological traits.
  
  
  RESULTS
  Here, we not only identify 11 AGOs in N. attenuata, we further annotate 133 genes in 17 plant species, previously not annotated in the Phytozome database, to increase the number of plant AGOs to 263 genes from 37 plant species. We report the phylogenetic classification, expansion, and diversification of AGOs in the plant kingdom, which resulted in the following hypothesis about their evolutionary history: an ancestral AGO underwent duplication events after the divergence of unicellular green algae, giving rise to four major classes with subsequent gains/losses during the radiation of higher plants, resulting in the large number of extant AGOs. Class-specific signatures in the RNA-binding and catalytic domains, which may contribute to the functional diversity of plant AGOs, as well as context-dependent changes in sequence and domain architecture that may have consequences for gene function were found.
  
  
  CONCLUSIONS
  Together, the results demonstrate that the evolution of AGOs has been a dynamic process producing the signatures of functional diversification in the smRNA pathways of higher plants.
authors.affiliation: Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, Nadia, 741246, West Bengal, India. rks12rs025@iiserkol.ac.in.
authors.forename: Ravi K
authors.initials: RK
authors.lastname: Singh
authors.affiliation: Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany. gase@ice.mpg.de.
authors.forename: Klaus
authors.initials: K
authors.lastname: Gase
authors.affiliation: Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany. baldwin@ice.mpg.de.
authors.forename: Ian T
authors.initials: IT
authors.lastname: Baldwin
authors.affiliation: Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, Nadia, 741246, West Bengal, India. sppandey@iiserkol.ac.in.
authors.forename: Shree P
authors.initials: SP
authors.lastname: Pandey
mesh_terms: D000595:Amino Acid Sequence; D060565:Argonaute Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D010944:Plants / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D014026:Nicotiana / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D060565:Argonaute Proteins; D010940:Plant Proteins