Modeling gene and genome duplications in eukaryotes.

By Steven Maere, Stefanie de Bodt, Jeroen Raes, T. Casneuf, M. Van Montagu, Martin Kuiper, Y. Van de Peer. Proceedings of the National Academy of Sciences of the United States of America, 2005

925 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/50754196680fd8729e74e656471fefee0136c275

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Citations in the corpus

Whole-genome duplication in teleost fishes and its evolutionary consequences (2014, background): “Strong evidence mainly obtained in plants, yeast and unicellular eukaryotes has been collected that duplicate genes with certain properties are over-retained after WGD events (for example, see Seoighe and Wolfe 1999; Papp et al. 2003; Maere et al. 2005; Aury et al. 2006).”
Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade (2006, background): “V alentin and O lmstead 2003; M artins and B arkman 2005).”
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007, methodology): “We assume three genome duplications to have occurred in both poplar and Arabidopsis, as proposed earlier [12,98,105], one of which has been shared by all dicots (and possible also by the monocots, see [98]), one that has been shared by Arabidopsis and poplar, but not Vitis , and one that has been…”
Widespread genome duplications throughout the history of flowering plants. (2006, background): “results to analyses of all paralogous pairs (Fig. 2B; Lynch and Conery 2000; Blanc et al. 2003; Maere et al. 2005), suggesting that 6000 unigenes are sufficient for estimating Ks distributions for the other species in this study (Table 2).”
Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. (2009, background): “Underretained (overfractionated) gene categories included families encoding ancient “conserved biological functions” (62) such as DNA metabolism, nuclease activity, and RNA binding.”
Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice (2006, background): “Surprisingly, the process of gene loss is nonrandom with respect to function, because genes that are retained as duplicates are enriched for functions related to transcription, signal transduction, and development [1,2].”
The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications (2018, background): “Indeed, parallel evidence from the study of patterns of gene retention following allo-polyploidization (Maere et al., 2005; Thomas et al., 2006; Coate et al., 2011) or frommore manageable experimental systems like the X chromosome (Birchler, 2014) support the idea that dosage responses are selective”
The evolutionary significance of ancient genome duplications (2009, background): “Transcriptional and developmental regulators and signal transducers have been preferentially retained in duplicate after all genome duplications in Arabidopsis thaliana”