Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion

Julie Jacquemin, Jetty S.S. Ammiraju, Georg Haberer, Dean D. Billheimer, Yeisoo Yu, Liana C. Liu, Luis F. Rivera, Klaus Mayer, Mingsheng Chen, Rod A. Wing

Research output: Contribution to journalArticle

25 Scopus citations

Abstract

In analyzing gene families in the whole-genome sequences available for O. sativa (AA), O. glaberrima (AA), and O. brachyantha (FF), we observed large size expansions in the AA genomes compared to FF genomes for the super-families F-box and NB-ARC, and five additional families: the Aspartic proteases, BTB/POZ proteins (BTB), Glutaredoxins, Trypsin α-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.

Original languageEnglish (US)
Pages (from-to)642-656
Number of pages15
JournalMolecular Plant
Volume7
Issue number4
DOIs
StatePublished - Apr 2014

Keywords

  • Oryza
  • duplicated gene evolution.
  • gene family expansion
  • tandem duplication

ASJC Scopus subject areas

  • Molecular Biology
  • Plant Science

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    Jacquemin, J., Ammiraju, J. S. S., Haberer, G., Billheimer, D. D., Yu, Y., Liu, L. C., Rivera, L. F., Mayer, K., Chen, M., & Wing, R. A. (2014). Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. Molecular Plant, 7(4), 642-656. https://doi.org/10.1093/mp/sst149