15 MYA of evolution in the Oryza genus shows extensive gene family expansion
Authors
1 Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
2 MIPS/IBIS, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
3 Arizona Statistics Consulting Laboratory, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
4 State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
Mol. Plant (2013) doi: 10.1093/mp/sst149 First published online: November 8, 2013
Corresponding author: Rod A. Wing email: rwing@ag.arizona.edu Tel. (+1) 520.626.9595 Fax. (+1) 520.621.1259
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 expansion in the AA genomes compared to FF genomes for the super-families F-box and NB-ARC, and 5 additional families: the Aspartic proteases, BTB/POZ proteins, 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 genes 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.
