Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell

Doyle, Jeff J.; Coate, Jeremy E.

doi:10.1086/700636

Cited by 258 publications

(335 citation statements)

References 518 publications

Supporting

Mentioning

332

Contrasting

Unclassified

Order By: Relevance

“…One of the most well-established direct impacts of polyploidy is an increase in cell size (Beaulieu et al, 2008;Doyle and Coate, 2019), which likely underlies the increases in nodule area and N-fixation zone area in nodules produced by neotetraploid M. sativa subsp. caerulea plants.…”

Section: Discussionmentioning

confidence: 99%

“…Fundamental changes that directly result from an increase in ploidy, such as larger cell size, faster photosynthetic rate, and duplications of genes that function in mutualism establishment and maintenance (Levin, ; Beaulieu et al., ; Maherali et al., ; Young et al., ; Martin and Husband, ; Li et al., ; Doyle and Coate, ), could alter legume interactions with rhizobium. Specifically, polyploid plants that have larger cells or more resources to allocate to the mutualism might host higher quality or a greater quantity of rhizobial symbionts relative to diploids, resulting in increased host benefits obtained (Levin, ; reviewed by Forrester and Ashman, 2018a; Forrester, ).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Autopolyploidy alters nodule‐level interactions in the legume–rhizobium mutualism

Forrester

Ashman

2019

American J of Botany

View full text Add to dashboard Cite

Premise Polyploidy is a major genetic driver of ecological and evolutionary processes in plants, yet its effects on plant interactions with mutualistic microbes remain unresolved. The legume–rhizobium symbiosis regulates global nutrient cycles and plays a role in the diversification of legume species. In this mutualism, rhizobia bacteria fix nitrogen in exchange for carbon provided by legume hosts. This exchange occurs inside root nodules, which house bacterial cells and represent the interface of legume–rhizobium interactions. Although polyploidy may directly impact the legume–rhizobium mutualism, no studies have explored how it alters the internal structure of nodules. Methods We created synthetic autotetraploids using Medicago sativa subsp. caerulea. Neotetraploid plants and their diploid progenitors were singly inoculated with two strains of rhizobia, Sinorhizobium meliloti and S. medicae. Confocal microscopy was used to quantify internal traits of nodules produced by diploid and neotetraploid plants. Results Autotetraploid plants produced larger nodules with larger nitrogen fixation zones than diploids for both strains of rhizobia, although the significance of these differences was limited by power. Neotetraploid M. sativa subsp. caerulea plants also produced symbiosomes that were significantly larger, nearly twice the size, than those present in diploids. Conclusions This study sheds light on how polyploidy directly affects a plant–bacterium mutualism and uncovers novel mechanisms. Changes in plant–microbe interactions that directly result from polyploidy likely contribute to the increased ability of polyploid legumes to establish in diverse environments.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Autopolyploidy alters nodule‐level interactions in the legume–rhizobium mutualism

Forrester

Ashman

2019

American J of Botany

View full text Add to dashboard Cite

show abstract

“…In comparison with the trans action of hybridization per se , how genome doubling alters homoeolog gene expression is complicated by multiple issues of scaling and stoichiometry. With the increase of DNA content accompanying allopolyploidy, imperfect proportionalities and nonlinear relationships with cellular and nuclear volumes set in motion a cascade of stoichiometric imbalances (among, for example, transcriptional machineries and TFs), which collectively alter gene expression (Doyle & Coate, ). Because the physiochemical responses of individual homoeologs vary from gene to gene, it is not yet possible to systematically predict how stoichiometric imbalances triggered by genome merger and doubling will impact regulatory interactions.…”

Section: Additional Modeling and Other Molecular Tools Are Needed To mentioning

confidence: 99%

“…Because current methods such as RNA‐seq rely on per‐transcriptome normalization to compare expression level across samples, there is an underlying assumption of equal transcriptome size . This assumption, however, probably does not hold in most cases (Coate & Doyle, , ; Visger et al ., ; Doyle & Coate, ), due to the multiple stoichiometric and volumetric cascades that affect gene expression following hybridization and doubling. As shown in Fig.…”

Section: The Extended Cis–trans Framework and Expression Patterns In mentioning

confidence: 99%

Cis–trans controls and regulatory novelty accompanying allopolyploidization

Wendel

2018

New Phytologist

View full text Add to dashboard Cite

Summary Allopolyploidy is a prevalent process in plants, having important physiological, ecological and evolutionary consequences. Transcriptomic responses to genomic merger and doubling have been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression‐level dominance and revamping of co‐expression networks. Notwithstanding the foregoing, there remains a need to develop a conceptual framework that will stimulate a deeper understanding of these diverse phenomena and their mechanistic interrelationships. Here we introduce considerations relevant to this framework with a focus on cis–trans interactions among duplicated genes and alleles in hybrids and allopolyploids. By extending classic allele‐specific expression analysis to the allopolyploid level, we distinguish the distinct effects of progenitor regulatory interactions from the novel intergenomic interactions that arise from genome merger and allopolyploidization. This perspective informs experiments designed to reveal the molecular genetic basis of gene regulatory control, and will facilitate the disentangling of genetic from epigenetic and higher‐order effects that impact gene expression. Finally, we suggest that the extended cis–trans model may help conceptually unify several presently disparate hallmarks of allopolyploid evolution, including genome‐wide expression dominance and biased fractionation, and lead to a new level of understanding of phenotypic novelty accompanying polyploidy.

show abstract

“…Whole genome duplication (WGD) and hybridisation are key drivers of genomic novelty, promoting diversification in all kingdoms of life [1][2][3] . Recent progress in evolutionary genomics underscores the ubiquity of WGD at both ancient and recent time scales 4 , and population genomic approaches reveal widespread evidence of gene flow between the most diverse of species 5,6 .…”

Section: Introductionmentioning

confidence: 99%

Interspecific introgression mediates adaptation to whole genome duplication

Marburger

Monnahan

Seear

et al. 2019

Preprint

View full text Add to dashboard Cite

Adaptive gene flow is a consequential evolutionary phenomenon across all kingdoms of life.While recognition of widespread gene flow is growing, examples lack of bidirectional gene flow mediating adaptations at specific loci that cooperatively manage core cellular processes.We previously described concerted molecular changes among physically interacting members of the meiotic machinery controlling crossover number and distribution upon adaptation to whole genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that escape from extinction following the trauma of WGD was mediated by adaptive gene flow between A. arenosa and its congener Arabidopsis lyrata. We show that A. lyrata underwent WGD more recently than A. arenosa, indicating that specific pre-adapted alleles donated by A. arenosa underwent selection and rescued the nascent A. lyrata tetraploids from early extinction. At the same time, we detect specific signals of gene flow in the opposite direction at other functionally interacting gene coding loci that display dramatic signatures of selective sweep in both tetraploid species. Cytological analysis shows that A. lyrata tetraploids exhibit similar levels of meiotic stability as A. arenosa tetraploids. Taken together, these data indicate that bidirectional gene flow allowed for an escape from extinction of the young autopolyploids, especially the rare tetraploid A. lyrata, and suggest that the merger of these species is greater than the sum of their parts.

show abstract

Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell

Cited by 258 publications

References 518 publications

Autopolyploidy alters nodule‐level interactions in the legume–rhizobium mutualism

Autopolyploidy alters nodule‐level interactions in the legume–rhizobium mutualism

Cis–trans controls and regulatory novelty accompanying allopolyploidization

Interspecific introgression mediates adaptation to whole genome duplication

Contact Info

Product

Resources

About