Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.
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.
Department of Biology, Indiana University, Bloomington, Indiana 47405, USA. rinnes@indiana.edu
Roger W
RW
Innes
Carine
C
Ameline-Torregrosa
Tom
T
Ashfield
Ethalinda
E
Cannon
Steven B
SB
Cannon
Ben
B
Chacko
Nicolas W G
NW
Chen
Arnaud
A
Couloux
Anita
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Dalwani
Roxanne
R
Denny
Shweta
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Deshpande
Ashley N
AN
Egan
Natasha
N
Glover
Christian S
CS
Hans
Stacy
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Howell
Dan
D
Ilut
Scott
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Jackson
Hongshing
H
Lai
Jafar
J
Mammadov
Sara Martin
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Del Campo
Michelle
M
Metcalf
Ashley
A
Nguyen
Majesta
M
O'Bleness
Bernard E
BE
Pfeil
Ram
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Podicheti
Milind B
MB
Ratnaparkhe
Sylvie
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Samain
Iryna
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Sanders
Béatrice
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Ségurens
Mireille
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Sévignac
Sue
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Sherman-Broyles
Vincent
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Thareau
Dominic M
DM
Tucker
Jason
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Walling
Adam
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Wawrzynski
Jing
J
Yi
Jeff J
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Doyle
Valérie
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Geffroy
Bruce A
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Roe
M A Saghai
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Maroof
Nevin D
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Young
D002503:Centromere / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial; D018744:DNA, Plant / Q000737:chemistry; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D007113:Immunity, Innate / Q000235:genetics; D005810:Multigene Family; D016254:Mutagenesis, Insertional; D027805:Phaseolus / Q000235:genetics; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics; D011123:Polyploidy; D018626:Retroelements; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
D018744:DNA, Plant; D018626:Retroelements