TY - JOUR
T1 - Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion
AU - Jacquemin, Julie
AU - Ammiraju, Jetty S.S.
AU - Haberer, Georg
AU - Billheimer, Dean D.
AU - Yu, Yeisoo
AU - Liu, Liana C.
AU - Rivera, Luis F.
AU - Mayer, Klaus
AU - Chen, Mingsheng
AU - Wing, Rod A.
N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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. © 2013 The Author.
AB - 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. © 2013 The Author.
UR - https://linkinghub.elsevier.com/retrieve/pii/S1674205214606717
UR - http://www.scopus.com/inward/record.url?scp=84898764164&partnerID=8YFLogxK
U2 - 10.1093/mp/sst149
DO - 10.1093/mp/sst149
M3 - Article
SN - 1752-9867
VL - 7
JO - Molecular Plant
JF - Molecular Plant
IS - 4
ER -