Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling

Sankoff, David; Zheng, Chunfang; Wang, Baoyong; Najar, Carlos Fernando Buen Abad

doi:10.1186/1471-2105-16-s17-s9

Cited by 3 publications

(3 citation statements)

References 9 publications

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“…Two orthogonal approaches to the study of fractionation-duplicate gene loss after polyploidization-focus on one hand on the decrease over time of the number of surviving duplicate pairs [1][2][3][4][5][6][7] and, on the other hand, the number of syntenically consecutive pairs lost after the event [8][9][10][11][12]. In this paper, we integrate the two in a single model, enabling for the first time inference of all parameters, with wide application to flowering plant genomes.…”

Section: Introductionmentioning

confidence: 99%

Integrated synteny- and similarity-based inference on the polyploidization–fractionation cycle

Zhang

Zheng

et al. 2021

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Whole-genome doubling, tripling or replicating to a greater degree, due to fixation of polyploidization events, is attested in almost all lineages of the flowering plants, recurring in the ancestry of some plants two, three or more times in retracing their history to the earliest angiosperm. This major mechanism in plant genome evolution, which generally appears as instantaneous on the evolutionary time scale, sets in operation a compensatory process called fractionation, the loss of duplicate genes, initially rapid, but continuing at a diminishing rate over millions and tens of millions of years. We study this process by statistically comparing the distribution of duplicate gene pairs as a function of their time of creation through polyploidization, as measured by sequence similarity. The stochastic model that accounts for this distribution, though exceedingly simple, still has too many parameters to be estimated based only on the similarity distribution, while the computational procedures for compiling the distribution from annotated genomic data is heavily biased against earlier polyploidization events—syntenic ‘crumble’. Other parameters, such as the size of the initial gene complement and the ploidy of the various events giving rise to duplicate gene pairs, are even more inaccessible to estimation. Here, we show how the frequency of unpaired genes, identified via their embedding in stretches of duplicate pairs, together with previously established constraints among some parameters, adds enormously to the range of successive polyploidization events that can be analysed. This also allows us to estimate the initial gene complement and to correct for the bias due to crumble. We explore the applicability of our methodology to four flowering plant genomes covering a range of different polyploidization histories.

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Section: Introductionmentioning

confidence: 99%

Integrated synteny- and similarity-based inference on the polyploidization–fractionation cycle

Zhang

Zheng

et al. 2021

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“…In this paper, we model the process as the deletion of segments from the real line, with a biologically realistic treatment afforded to overlapping deletions. Previous work focused on the difficult question of how many overlapping deletion events are responsible for each contiguous deleted region [2–4], but was not able to account analytically for the dynamics of the process.…”

Section: Introductionmentioning

confidence: 99%

“…For the one-sided model, a closed form solution of how many deletion events contribute to a deleted region after a single event (i.e., at a single step in the fractionation process) was obtained in [4]. …”

Section: Introductionmentioning

confidence: 99%

A continuous analog of run length distributions reflecting accumulated fractionation events

Sankoff

2016

BMC Bioinformatics

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BackgroundWe propose a new, continuous model of the fractionation process (duplicate gene deletion after polyploidization) on the real line. The aim is to infer how much DNA is deleted at a time, based on segment lengths for alternating deleted (invisible) and undeleted (visible) regions.ResultsAfter deriving a number of analytical results for “one-sided” fractionation, we undertake a series of simulations that help us identify the distribution of segment lengths as a gamma with shape and rate parameters evolving over time. This leads to an inference procedure based on observed length distributions for visible and invisible segments.ConclusionsWe suggest extensions of this mathematical and simulation work to biologically realistic discrete models, including two-sided fractionation.

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Evolution of MicroRNA Biogenesis Genes in the Sterlet (Acipenser ruthenus) and Other Polyploid Vertebrates

Fofanov

Prokopov

Kuhl

et al. 2020

IJMS

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MicroRNAs play a crucial role in eukaryotic gene regulation. For a long time, only little was known about microRNA-based gene regulatory mechanisms in polyploid animal genomes due to difficulties of polyploid genome assembly. However, in recent years, several polyploid genomes of fish, amphibian, and even invertebrate species have been sequenced and assembled. Here we investigated several key microRNA-associated genes in the recently sequenced sterlet (Acipenser ruthenus) genome, whose lineage has undergone a whole genome duplication around 180 MYA. We show that two paralogs of drosha, dgcr8, xpo1, and xpo5 as well as most ago genes have been retained after the acipenserid-specific whole genome duplication, while ago1 and ago3 genes have lost one paralog. While most diploid vertebrates possess only a single copy of dicer1, we strikingly found four paralogs of this gene in the sterlet genome, derived from a tandem segmental duplication that occurred prior to the last whole genome duplication. ago1,3,4 and exportins1,5 look to be prone to additional segment duplications producing up to four-five paralog copies in ray-finned fishes. We demonstrate for the first time exon microsatellite amplification in the acipenserid drosha2 gene, resulting in a highly variable protein product, which may indicate sub- or neofunctionalization. Paralogous copies of most microRNA metabolism genes exhibit different expression profiles in various tissues and remain functional despite the rediploidization process. Subfunctionalization of microRNA processing gene paralogs may be beneficial for different pathways of microRNA metabolism. Genetic variability of microRNA processing genes may represent a substrate for natural selection, and, by increasing genetic plasticity, could facilitate adaptations to changing environments.

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Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling

Cited by 3 publications

References 9 publications

Integrated synteny- and similarity-based inference on the polyploidization–fractionation cycle

Integrated synteny- and similarity-based inference on the polyploidization–fractionation cycle

A continuous analog of run length distributions reflecting accumulated fractionation events

Evolution of MicroRNA Biogenesis Genes in the Sterlet (Acipenser ruthenus) and Other Polyploid Vertebrates

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