Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

By James c. Schnable, Nathan M. Springer, Michael Freeling. Proceedings of the National Academy of Sciences of the United States of America, 2011

653 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/b8914e1519991aee4969a6e5599db4a80074bb4b

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Citations in the corpus

Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “However, this difference in expression could result from fractionation among WGD duplicates (Schnable et al., 2011) that may not be subject to selection, at least initially.”
The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates (2011, background): “…sativa BGIOSGA010900, Oryza indica BRADI1G64687, Brachypodium distachyon Rosids: 11 homologs Figure 2 (a) A dot blot indicating homologous genes between maize and sorghum, following Schnable et al. (2011) and based on SynMap (http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl) with default settings.”
Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell (2019, background): “It operates primarily on the repetitive portion of the genome (e.g., RennyByfield et al. 2011) but also involves the process of gene fractionation (Langham et al. 2004; Schnable et al. 2011; Bird et al. 2018).”
Improved maize reference genome with single-molecule technologies (2017, neutral): “Gene loss in maize has primarily been considered in the context of polyploidy and func tional redundancy 16 , but we found that despite its polyploidy, maize has lost a larger proportion (14”
Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes (2011, background): “3A) shows that a large number of gene families (1829) have two members refl ective of an ancient whole genome duplication in maize and previously identifi ed nearly identical paralogs (Schnable et al., 2011, 2009).”
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].”
Novel Methods to Optimize Genotypic Imputation for Low‐Coverage, Next‐Generation Sequence Data in Crop Plants (2014, background): “Maize is not unique in this respect; many agronomically important crop plants show a similar pattern of high structural variation and allelic diversity (Bhullar et al., 2010; Hurwitz et al., 2010; Schnable et al., 2011; Ramu et al., 2013; Das et al., 2013).”
Draft genome of the living fossil Ginkgo biloba (2016, background): “insertions tend to accumulate in genes that are expressed at lower levels [41], which may be driven by negative selection due to increased transcriptional cost”