Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean  

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/homoeologuespecific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.The comparative approach to studying genes and genomes is a powerful method for addressing both

Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean

“…The median Ks values of Gm-Gm paralogs within pair A (0.16) and pair B (0.17) were almost identical to the Ks values previously reported for the recent polyploidy event (Blanc and Wolfe, 2004;Schlueter et al, 2004Schlueter et al, , 2006Schlueter et al, , 2007bInnes et al, 2008;Shin et al, 2008; Van et al, 2008). The Ks value of Gm-Gm paralogs between combinations of A and B pairs were greater (0.67, 0.66, 0.66, and 0.62) than the intrapair values.…”

“…Among 268 predicted genes in GmA, 189 were present in GmA#, indicating that 71% of the duplicated genes formed by the recent polyploidy event have been conserved. A similar rate of retention has been documented for Rpg1-b homeologous regions (Innes et al, 2008). Furthermore, among 268 genes, 21% and 24% of genes found in GmB (56 genes) and GmB# (63 genes), respectively, were conserved, showing that nearly three-quarters of genes duplicated by the ancient polyploidy event have been lost.…”

“…The Ks value of Gm-Gm paralogs between combinations of A and B pairs were greater (0.67, 0.66, 0.66, and 0.62) than the intrapair values. This suggests that these duplicate gene pairs resulted from the ancient polyploidy event (Blanc and Wolfe, 2004;Schlueter et al, 2004;Pfeil et al, 2005;Innes et al, 2008;Shin et al, 2008). The average nucleotide and amino acid identities between Gm-Gm paralogs produced by the recent polyploidy event were 90% and 87.4%, respectively.…”

“…Genome analysis with 17 homeologous BAC clones supports whole-genome duplication (WGD) rather than segmental duplication in soybean (Schlueter et al, 2007a). Recently, three homeologous regions centered on the Rpg1-b gene were analyzed, and a maximum of four homeologous regions in modern Glycine species were proposed (Innes et al, 2008). The presence of lipoxygenase families in four homeologous regions provides support for the hypothesis that the quadruplicated genome structure of soybean is derived from two different rounds of polyploidy .…”

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

“…soja versus G. max: genomic basis of agronomic traits R-genes with NBS domains mediate effector-triggered immunity acting as detectors for pathogen virulence proteins 24 . The quantity of R-genes with a given domain architecture and the number of unique domain architectures varied between the two species.…”