Polyploidy and the proteome

Abstract

Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Pure polyploidy: Closing the gaps in autopolyploid research

“…). Allopolyploids in Arabidopsis, Brassica , Tragopogon , Gossypium , Spartina , and Triticum have been used to investigate the immediate and long‐term genetic, epigenetic, genomic, proteomic, physiological, morphological, and ecological effects of WGD, as well as to explore the role of allopolyploidy in speciation, domestication, and invasion (reviews of these species and topics include: Madlung, ; Aïnouche & Wendel, ; Bomblies & Madlung, ; Renny‐Byfield & Wendel, ; Yoo et al, ; Song & Chen, ; Soltis et al, ). Comparable research in autopolyploids is sparse, however, and disparate fields of inquiry are rarely addressed within the same autopolyploid research system.…”

Towards the new normal: Transcriptomic and genomic changes in the two subgenomes of a 100,000 years old allopolyploid,Capsella bursa-pastoris

“…These challenges are first associated with the initial hybridization between two already divergent genomes that have now to start working together, implying, among other things, important changes of the meiotic machinery and of gene expression patterns (12). The magnitude of gene expression changes has been reported to vary substantially across polyploid species, from minor modifications (13,14) to so-called "transcriptomic shock" (7). The balance in expression pattern between the two subgenomes also seems to be highly variable and ranges from non-additivity, such as extreme expression dominance of one of the ancestral genomes over the other, to the additivity of their expression contributions (15,16), and it also evolves through time.…”

Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change InArabidopsis thaliana

“…Such decoupling is evident in response to polyploidy because not all genes show identical expression responses following duplication -whether measured at the level of transcript abundance (e.g. Pirrello et al (2018);Hou et al (2018);Guo et al (1996); Riddle et al (2006); Robinson et al (2018); Stupar et al (2007); Yu et al (2010), additional references in Doyle and Coate (2019)) or protein abundance (Birchler and Newton 1981;Yao et al 2011;Zhu et al 2012;Soltis et al 2016;55 Deng et al 2017;Wang et al 2017;Yan et al 2017). Consequently, WGD does not necessarily preserve protein dosage balance, and the extent to which dosage responses following WGD are coordinated amongst genes encoding interacting proteins is unknown.…”