Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics.

By Andrew H. Paterson, John E. Bowers, Brad A. Chapman. Proceedings of the National Academy of Sciences of the United States of America, 2004

1,017 citations recorded by the source corpus.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/f1541f18df142855c86bbac168548f303fa74f61

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Citations in the corpus

Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12 (2005, methodology): “Sequence-based alignment of the rice and sorghum genomes has revealedmacrocolinearity between sorghum chromosome 8 and rice chromosome 12 (Paterson et al. 2004a).”
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol (2013, background): “Maize is a large and complex genome, which experienced multiple genome duplication events [41,42], has a large amount of repetitive sequence, numerous PAVs [23,43,44], with only about 50% overlap in sequence content between any two unrelated inbred lines [45,46].”
Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae) (2009, background): “It is not clear yet whether these paralogs are a consequence of a paleoduplication in the Poaceae (Paterson et al. 2004) or instead resulted from independent individual gene duplication in the Chloridoideae subfamily.”
Evolutionary genetics of genome merger and doubling in plants. (2008, methodology): “However, such buffering still markedly affects diversity among modern ecotypes of A. thaliana and subspecies of Oryza sativa (10), species whose genomes were shaped by duplications that occurred 60 million years or more prior to speciation (12, 80).”
Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice (2006, background): “The evidence for polyploidy in rice is convincing based on collinearity among chromosomes [5], but Ks distributions initially failed to uncover a peak corresponding to a whole genome duplication event [2].”
The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications (2018, background): “There is clear evidence of WGD in the ancestry of most plant lineages (Vision et al., 2000; Bowers et al., 2003; Paterson et al., 2004; Schlueter et al., 2004; Pfeil et al., 2005; Barker et al., 2008; Burleigh et al., 2008; Shi et al., 2010).”
Polyploidy and Crop Improvement (2006, background): “, 2003), even with its quintessentially streamlined genome, as well as an ancient duplication at the base of the grasses (Paterson et al., 2004) and a more recent superimposition of an additional polyploidization in the maize lineage (Gaut and Doebley, 1997; Gaut, 2001), legumes (Shoemaker et al.”
The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome (2011, background): “These recent genome duplications are superimposed on an additional duplication shared by most if not all cereals (Paterson et al. 2004).”
SyMAP v3.4: a turnkey synteny system with application to plant genomes (2011, background): “The grasses share a duplication event 70Mya followed by divergence 50Mya (41).”
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. (2005, background): “This process of gene loss during evolution can proceed differently in different post-WGD species, a situation referred to as differential gene loss (Lundin 1993; Seoighe and Wolfe 1999; Fischer et al. 2001; Paterson et al. 2004).”
Polyploidy and angiosperm diversification. (2009, methodology): “Placement of inferred genome duplication event detected in Poaceae by Paterson et al. (2004) ; summary tree modifi ed from that of the Grass Phylogeny Working Group (2001) .”
Widespread genome duplications throughout the history of flowering plants. (2006, background): “These results corroborate previous evidence that ancient genome duplication events are not always detectable in analyses of Ks distributions (Blanc and Wolfe 2004; Paterson et al. 2004a ).”
Developmental Gene Evolution and the Origin of Grass Inflorescence Diversity (2006, background): “The FEA2/CLV2 duplicates produced by the grass (Paterson et al., 2004; Yu et al., 2005), eudicot, and Brassicaceae (Bowers et al., 2003) duplication events therefore must have been lost during evolutionary time.”