Dynamics of Duplicated Gene Expression in Polyploid Cotton

Adams, Keith L.; Wendel, Jonathan F.

doi:10.1002/9781118552872.ch11

Cited by 6 publications

(3 citation statements)

References 32 publications

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“…Similarly, recent work in cotton has demonstrated that expression dominance between homeologs occurs immediately following tetraploidization and increases over time (Adams and Wendel 2013;Yoo et al 2013). Interestingly, we find that when defined using statistically significant differential expression test- Figure 4.…”

Section: Discussionmentioning

confidence: 58%

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

2014

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Whole-genome duplications are a widespread feature of plant genome evolution, having been detected in all flowering plant lineages. Despite the prevalence of these events, the extent to which duplicated genes (homeolog gene pairs) functionally diverge (neofunctionalization) is unclear. We present a genome-wide analysis of molecular evolution and regulatory neofunctionalization in maize (Zea mays L.). We demonstrate that 13% of all homeolog gene pairs in maize are regulatory neofunctionalized in leaves, and that regulatory neofunctionalized genes experience enhanced purifying selection. We show that significantly more genes have been regulatory neofunctionalized in foliar leaves than in husk leaves and that both leaf types have experienced selection for distinct functional roles. Furthermore, we demonstrate that biased subgenome expression dominance occurs only in the presence of regulatory neofunctionalization and that in nonregulatory neofunctionalized genes subgenome dominance is progressively acquired during development. Taken together, our study reveals several novel insights into the evolution of maize, genes, and gene expression, and provides a general model for gene evolution following whole-genome duplication in plants.

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Section: Discussionmentioning

confidence: 58%

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

2014

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“…It was widely recognized that WGD has profound effects on the genome constitution of plants [ 8 , 11 , 15 , 17 , 19 , 63 ]. The notable feature of polyploidy is that it would increase the copy numbers of a given gene.…”

Section: Discussionmentioning

confidence: 99%

The impacts of polyploidy, geographic and ecological isolations on the diversification of Panax (Araliaceae)

Shi

et al. 2015

BMC Plant Biol

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BackgroundPanax L. is a medicinally important genus within family Araliaceae, where almost all species are of cultural significance for traditional Chinese medicine. Previous studies suggested two independent origins of the East Asia and North America disjunct distribution of this genus and multiple rounds of whole genome duplications (WGDs) might have occurred during the evolutionary process.ResultsWe employed multiple chloroplast and nuclear markers to investigate the evolution and diversification of Panax. Our phylogenetic analyses confirmed previous observations of the independent origins of disjunct distribution and both ancient and recent WGDs have occurred within Panax. The estimations of divergence time implied that the ancient WGD might have occurred before the establishment of Panax. Thereafter, at least two independent recent WGD events have occurred within Panax, one of which has led to the formation of three geographically isolated tetraploid species P. ginseng, P. japonicus and P. quinquefolius. Population genetic analyses showed that the diploid species P. notoginseng harbored significantly lower nucleotide diversity than those of the two tetraploid species P. ginseng and P. quinquefolius and the three species showed distinct nucleotide variation patterns at exon regions.ConclusionOur findings based on the phylogenetic and population genetic analyses, coupled with the species distribution patterns of Panax, suggested that the two rounds of WGD along with the geographic and ecological isolations might have together contributed to the evolution and diversification of this genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0669-0) contains supplementary material, which is available to authorized users.

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“…The role of polyploidy in facilitating changes in gene expression, through expression level divergence, altered expression patterns (e.g., across tissue types), and/or the generation of unique splice variants, is arguably one of the most important research topics in the field today (e.g., Liu et al., ; Adams et al., ; Chelaifa et al., ; Dong and Adams, ; Adams and Wendel, ; Ainouche et al., ; Buggs, ; Buggs et al., ; Rambani et al., ; Bottani et al., ; see Yoo et al., for review). Due in part to early and influential researchers considering autopolyploids (duplication of the same or highly similar genomes) to be infrequent and maladaptive (Stebbins, ; Grant, ), they have historically been understudied relative to their allopolyploid (duplication of two or more divergent genomes) counterparts, leading to few studies of gene expression following autopolyploidy.…”

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confidence: 99%

Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass

Visger

Wong

Zhang

et al. 2019

American J of Botany

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PREMISE OF THE STUDY:Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance. METHODS:We use RNA spike-in standards in concert with cell size and density to identify and correct for differences in transcriptome size and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass.KEY RESULTS: In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentrationbased and therefore blind to differences in transcriptome size. CONCLUSIONS: While each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.

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Dynamics of Duplicated Gene Expression in Polyploid Cotton

Cited by 6 publications

References 32 publications

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

The impacts of polyploidy, geographic and ecological isolations on the diversification of Panax (Araliaceae)

Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass

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