Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

Schlueter, Jessica A.; Lin, Jer-Young; Schlueter, Shannon D.; Vasylenko-Sanders, Iryna F; Deshpande, Shweta; Yi, Jing; O’Bleness, Majesta; Roe, Bruce A.; Nelson, Rex T.; Scheffler, Brian E.; Jackson, Scott A.; Shoemaker, Randy C.

doi:10.1186/1471-2164-8-330

Cited by 128 publications

(111 citation statements)

References 66 publications

(113 reference statements)

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“…G. max is thought to be a diploidized tetraploid, following a genome duplication at $13 MYA (Blanc and Wolfe 2004; reviewed by Shoemaker et al 2006;Schlueter et al 2007).Therefore, most of the chromosome regions from which the BACs were derived are expected to have homeologous sequences elsewhere in the genome. Because these sequences often are detected as generally lower intensity signals when BACs are used in FISH (Pagel et al 2004;Walling et al 2006), we mapped secondary signals for most of the BAC probes by reexamining original or enhanced images from the mapping studies above (Table 1 and data not shown).…”

Section: Resultsmentioning

confidence: 99%

A Fluorescence in Situ Hybridization System for Karyotyping Soybean

et al. 2010

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The development of a universal soybean (Glycine max [L.] Merr.) cytogenetic map that associates classical genetic linkage groups, molecular linkage groups, and a sequence-based physical map with the karyotype has been impeded due to the soybean chromosomes themselves, which are small and morphologically homogeneous. To overcome this obstacle, we screened soybean repetitive DNA to develop a cocktail of fluorescent in situ hybridization (FISH) probes that could differentially label mitotic chromosomes in root tip preparations. We used genetically anchored BAC clones both to identify individual chromosomes in metaphase spreads and to complete a FISH-based karyotyping

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Section: Resultsmentioning

confidence: 99%

A Fluorescence in Situ Hybridization System for Karyotyping Soybean

et al. 2010

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“…Two BACs (Gm_UMb001_24D13 and Gm_UMb001_05F05) derived from soybean (Glycine max) homoeologous regions centered around the duplicated RFLP locus, pA711 (AQ842034), were sequenced in a previous study (Schlueter et al, 2007). These BACs were blasted (Altschul et al, 1990) against the Williams 82 BAC end sequence database to begin chromosome walking in the reference genotype.…”

Section: Bac Selectionmentioning

confidence: 99%

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

et al. 2010

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Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ;1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ;13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.

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“…Furthermore, this model supports a WGT rather than a WGD early in the evolution of these species. When this evidence of a Gamma WGT event is combined with the WGDs that occurred ;13 (Glycine) and 59 (legume) million years ago (Mya) in the evolutionary history of soybean (Schlueter et al, 2007;Schmutz et al, 2010), it is clear that soybean could contain as many as 12 copies of its ancestral genome with three sets of four homoeologous regions in soybean corresponding to a single ancestral region present before the Gamma event. We define these sets as being part of a Gamma hexaploidy lineage.…”

Section: Introductionmentioning

confidence: 99%

Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy

et al. 2011

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With the advent of high-throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. Numerous completed plant genome sequences enable characterization of patterns of the retention and evolution of genes within gene families due to multiple polyploidy events, gene loss and fractionation, and differential evolutionary pressures over time and across different gene families. In this report, we trace the changes that have occurred in 12 surviving homoeologous genomic regions from three rounds of polyploidy that contributed to the current Glycine max genome: a genome triplication before the origin of the rosids (~130 to 240 million years ago), a genome duplication early in the legumes (~58 million years ago), and a duplication in the Glycine lineage (~13 million years ago). Patterns of gene retention following the genome triplication event generally support predictions of the Gene Balance Hypothesis. Finally, we find that genes in networks with a high level of connectivity are more strongly conserved than those with low connectivity and that the enrichment of these highly connected genes in the 12 highly conserved homoeologous segments may in part explain their retention over more than 100 million years and repeated polyploidy events.

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Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

Cited by 128 publications

References 66 publications

A Fluorescence in Situ Hybridization System for Karyotyping Soybean

A Fluorescence in Situ Hybridization System for Karyotyping Soybean

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy

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