TY - JOUR
T1 - Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean
AU - Innes, Roger W.
AU - Ameline-Torregrosa, Carine
AU - Ashfield, Tom
AU - Cannon, Ethalinda
AU - Cannon, Steven B.
AU - Chacko, Ben
AU - Chen, Nicolas W.G.
AU - Couloux, Arnaud
AU - Dalwani, Anita
AU - Denny, Roxanne
AU - Deshpande, Shweta
AU - Egan, Ashley N.
AU - Glover, Natasha
AU - Hans, Christian S.
AU - Howell, Stacy
AU - Ilut, Dan
AU - Jackson, Scott
AU - Lai, Hongshing
AU - Mammadov, Jafar
AU - Del Campo, Sara Martin
AU - Metcalf, Michelle
AU - Nguyen, Ashley
AU - O'Bleness, Majesta
AU - Pfeil, Bernard E.
AU - Podicheti, Ram
AU - Ratnaparkhe, Milind B.
AU - Samain, Sylvie
AU - Sanders, Iryna
AU - Ségurens, Béatrice
AU - Sévignac, Mireille
AU - Sherman-Broyles, Sue
AU - Thareau, Vincent
AU - Tucker, Dominic M.
AU - Walling, Jason
AU - Wawrzynski, Adam
AU - Yi, Jing
AU - Doyle, Jeff J.
AU - Geffroy, Valérie
AU - Roe, Bruce A.
AU - Maroof, M. A.Saghai
AU - Young, Nevin D.
PY - 2008/12
Y1 - 2008/12
N2 - The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
AB - The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
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U2 - 10.1104/pp.108.127902
DO - 10.1104/pp.108.127902
M3 - Article
C2 - 18842825
AN - SCOPUS:57749105200
SN - 0032-0889
VL - 148
SP - 1740
EP - 1759
JO - Plant physiology
JF - Plant physiology
IS - 4
ER -