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Flagel LE, Udall J, Nettleton D, Wendel J. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol 6: 16

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
BMC Biology (Impact Factor: 7.98). 02/2008; 6(1):16. DOI: 10.1186/1741-7007-6-16
Source: PubMed

ABSTRACT

Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes.
We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 gene pairs. This comparison permitted partitioning of homoeolog expression biases into those arising from genomic merger and those resulting from polyploidy. Within allopolyploid Gossypium, approximately 24% of the genes with biased (unequal contributions from the two homoeologous copies) expression patterns are inferred to have arisen as a consequence of genomic merger, indicating that a substantial fraction of homoeolog expression biases occur instantaneously with hybridization. The remaining 76% of biased homoeologs reflect long-term evolutionary forces, such as duplicate gene neofunctionalization and subfunctionalization. Finally, we observed a greater number of genes biased toward the paternal D-genome and that expression biases have tended to increases during allopolyploid evolution.
Our results indicate that allopolyploidization entails significant homoeolog expression modulation, both immediately as a consequence of genomic merger, and secondarily as a result of long-term evolutionary transformations in duplicate gene expression.

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    • "Detection of different copies expected in these genomes may be challenging, because individual gene duplications (resulting in paralogs in both diploid and polyploid genomes) usually add an additional layer of complexity (Ainouche et al. 2012). Detection and analysis of homeologs is central to polyploidy research, and several studies have focused on the detection of different copies in polyploid genomes such as in Glycine (Ilut et al. 2012), Gossypium (Flagel et al. 2008; Salmon et al. 2009), Coffea (Combes et al. 2011) or Triticum (Akhunova et al. 2010) species. In these systems, the diploid parental (or related) representatives are known and can be used to identify duplicated homeologs in the allotetraploids. "
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    • "Differential geneexpression patterns among diploids and tetraploids have been studied to investigate the effects of natural and synthetic polyploidy for novel organ development and resistance to abiotic stresses (Chen and Ni, 2006; Doyle et al., 2008). The molecular basis of evolutionary advantage could be related to gene expression changes, which have been demonstrated in resynthesized polyploids in Arabidopsis (Wang et al., 2006), Brassica (Gaeta et al., 2009), and Gossypium (Flagel et al., 2008). RNA sequencing (RNA-seq) revealed the differential expression of ~50% of paralogues among 18 000 duplicated genes in soybean; the genes showed subfunctionalization on testing seven different tissues (Roulin et al., 2013). "
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    • "This discrepancy between transcriptomes in two newly-generated hexaploids might be due to the tissues examined (young seedling vs. flower bud) and/or genome constitutions (Hegarty et al., 2006, 2008). Preferential suppression of either genome usually takes place in interspecific hybrids and their amphidiploids (Wang et al., 2006; Flagel et al., 2008). Although sudden reunification of divergent genomes may induce genome instability (Adams et al., 2003; Wang et al., 2004; Doyle et al., 2008; Buggs et al., 2011), hybrid-or allopolyploidy-induced incompatibilities may be " settled " by gene expression modulation through chromatin modifications (Osborn et al., 2003; Chen et al., 2004; Ha et al., 2011), transcription factors (Barbash et al., 2003; Shi et al., 2012) and/or RNA interference in the selfing progeny (Wang et al., 2006; Ng et al., 2012). "
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