Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales

Mayfield‐Jones, Dustin; Washburn, Jacob D.; Arias, Tatiana; Edger, Patrick P.; Pires, J. Chris; Conant, Gavin C.

doi:10.1016/j.semcdb.2013.02.002

Cited by 40 publications

(44 citation statements)

References 143 publications

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“…Investigating the aftermath of WGDs across both deep and recent time scales provides clearer insight into the collective evolutionary processes that occur in a polyploid nucleus (Mayfield-Jones et al, 2013), including the emergence and establishment of subgenome dominance. Subgenome dominance has largely been investigated in ancient polyploids, including Arabidopsis (Thomas et al, 2006), maize , and Brassica (Cheng et al, 2016), which revealed the presence of a dominant subgenome with significantly greater gene content and which contributes more to the global transcriptome than the other subgenome(s).…”

Section: Discussionmentioning

confidence: 99%

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

et al. 2017

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Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained more genes and being more highly expressed, a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, <140-year-old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and progenitor species (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are reduced in regions near genes and within TEs in the first-generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and recessive subgenomes in the natural allopolyploid. Subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following hybridization. These findings provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events and may also contribute to uncovering the mechanistic basis of heterosis and subgenome dominance.

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Section: Discussionmentioning

confidence: 99%

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

et al. 2017

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“…These differences in genome size reflect underlying genomic processes such as (retro)transposon amplification and deletion and whole-genome duplication (polyploidy). All of these processes can influence molecular evolution, gene expression, and organismal phenotype (Neiman et al, 2009(Neiman et al, , 2013aGerstein, 2013;Mayfield-Jones et al, 2013;Ramsey and Ramsey, 2014;Dodsworth et al, 2015;Selmecki et al, 2015;Soltis and Soltis, 2016). Polyploidy in particular has been implicated in the remarkably successful radiations of angiosperms (Soltis et al, 2009;Jiao et al, 2011;Albert et al, 2013;Tank et al, 2015;Van de Peer et al, 2017) and teleost fish (Van de Peer et al, 2009;Braasch and Postlethwait, 2012).…”

Section: Future Research Prioritiesmentioning

confidence: 99%

Impacts of Nitrogen and Phosphorus: From Genomes to Natural Ecosystems and Agriculture

et al. 2017

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Nitrogen (N) and/or phosphorus (P) availability can limit growth of primary producers across most of the world's aquatic and terrestrial ecosystems. These constraints are commonly overcome in agriculture by applying fertilizers to improve yields. However, excessive anthropogenic N and P inputs impact natural environments and have far-reaching ecological and evolutionary consequences, from individual species up to entire ecosystems. The extent to which global N and P cycles have been perturbed over the past century can be seen as a global fertilization experiment with significant redistribution of nutrients across different ecosystems. Here we explore the effects of N and P availability on stoichiometry and genomic traits of organisms, which, in turn, can influence: (i) plant and animal abundances; (ii) trophic interactions and population dynamics; and (iii) ecosystem dynamics and productivity of agricultural crops. We articulate research priorities for a deeper understanding of how bioavailable N and P move through the environment and exert their ultimate impacts on biodiversity and ecosystem services.

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“…Changes in ploidy levels after WGD can lead to dramatic alterations at the cellular and phenotypic level (Mayfield-Jones et al 2013) and provide additional genetic variation for mutation, drift, and selection to act on. These evolutionary processes can result in new adaptations and species diversification (Van De Peer et al 2009; Storz et al 2013).…”

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confidence: 99%

“…Genome sequencing projects are increasingly revealing that WGD is widespread in many key lineages, such as flowering plants and vertebrates, and represents an ongoing phenomenon in many species (Otto and Whitton 2000; Van De Peer et al 2009). Understanding the processes governing the return to a diploid mode—diploidization—by comparing the genomes of species descended from a WGD event can provide insights into the event’s role in evolutionary innovation and persistence of duplicated regions (Jaillon et al 2009; Mayfield-Jones et al 2013). …”

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Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

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Brieuc

Devlin

et al. 2014

G3 Genes|Genomes|Genetics

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Whole genome duplication has been implicated in evolutionary innovation and rapid diversification. In salmonid fishes, however, whole genome duplication significantly pre-dates major transitions across the family, and re-diploidization has been a gradual process between genomes that have remained essentially collinear. Nevertheless, pairs of duplicated chromosome arms have diverged at different rates from each other, suggesting that the retention of duplicated regions through occasional pairing between homeologous chromosomes may have played an evolutionary role across species pairs. Extensive chromosomal arm rearrangements have been a key mechanism involved in re-dipliodization of the salmonid genome; therefore, we investigated their influence on degree of differentiation between homeologs across salmon species. We derived a linkage map for coho salmon and performed comparative mapping across syntenic arms within the genus Oncorhynchus, and with the genus Salmo, to determine the phylogenetic relationship between chromosome arrangements and the retention of undifferentiated duplicated regions. A 6596.7 cM female coho salmon map, comprising 30 linkage groups with 7415 and 1266 nonduplicated and duplicated loci, respectively, revealed uneven distribution of duplicated loci along and between chromosome arms. These duplicated regions were conserved across syntenic arms across Oncorhynchus species and were identified in metacentric chromosomes likely formed ancestrally to the divergence of Oncorhynchus from Salmo. These findings support previous studies in which observed pairings involved at least one metacentric chromosome. Re-diploidization in salmon may have been prevented or retarded by the formation of metacentric chromosomes after the whole genome duplication event and may explain lineage-specific innovations in salmon species if functional genes are found in these regions.

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Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales

Cited by 40 publications

References 143 publications

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

Impacts of Nitrogen and Phosphorus: From Genomes to Natural Ecosystems and Agriculture

Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

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