Abstract
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.
Highlights
We sequenced an approximately 1 million base-pair region in Glycine max centered on the Rpg1-b disease resistance gene and compared this region to a region duplicated 10-14 million years ago. These two regions were compared to homologous regions in several related legume species, which enabled us to determine how each of the duplicated regions in soybean has changed following polyploidy
The biggest change was in retroelement content, with homoeologue 2 having expanded to threefold the size of homoeologue 1
We focused our analyses on the Rpg1-b region, located on molecular linkage group F, because it is highly enriched in resistance genes belonging to the nucleotide binding-leucine rich repeat (NB-LRR) family (Ashfield et al, 2003; Ashfield et al, 2004) and we selected PI96983 for analysis because it had previously been shown to contain a suite of NB-LRRs in the Rpg1-b region quite distinct from Williams 82 based on Southern blot hybridizations (Jeong et al, 2001)
Summary
Note that we identified BAC clones in G. max cultivar Williams that appear to represent homoeologous regions derived from two different whole genome duplication events (Figure 1, see below) (Shoemaker et al, 2006). To confirm that H1 and H2 were derived from the most recent whole genome duplication event, we analyzed nucleotide substitution rates at silent sites (Ks) for 15 low copy genes spread over the entire aligned region (indicated by letters A through O in Figure 2A and described in Supplemental Table S3).
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