Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition.

By Michael Freeling. Annual Review of Plant Biology, 2009

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Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell (2019, background): “For gene dosage to be biologically meaningful, for example, to have consequences relevant for theories that account for differential retention of paralogues (e.g., Freeling 2009; Birchler and Veitia 2014), changes in copy number must have transcriptomic consequences (Coate et al. 2016).”
Homoeologs: What Are They and How Do We Infer Them? (2016, background): “For instance, some have used it not just in the context of allopolyploids but to relate duplicates created by autopolyploidy as well (for example, [25,26]).”
Whole-genome duplication in teleost fishes and its evolutionary consequences (2014, background): “Additionally, dosage sensitivity is expected to result in the retention of whole transcriptional networks that can as a whole get assigned a novel function (Freeling and Thomas 2006; Freeling 2009).”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, background): “Moreover transcription factor genes are preferentially retained following whole genome duplication events [29, 30] and thus transcription factor orthogroups are larger than average and contain multiple independent duplication events in multiple independent lineages that can cause some inference meth”