Gene Dosage Balance Immediately following Whole-Genome Duplication in Arabidopsis

Raju, Sunil Kumar Kenchanmane

doi:10.1105/tpc.20.00205

Cited by 4 publications

(1 citation statement)

References 4 publications

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“…Fourth, a combination of deleterious and beneficial mutations may lead to specialization, whereby each copy retains a subset of the ancestral function while acquiring a new one [ 13 , 14 ]. Despite the fact that mutations initiating the latter three retention mechanisms may take a while to manifest, dosage balance can serve as an intermediate state for preventing gene loss due to nonfunctionalization during this waiting period [ 15 – 19 ]. Polyploidization increases epigenome complexity and transcriptional regulation, resulting in genome evolution and greater adaptability to varying environments [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus

Sun,

Li,

Wang

2024

BMC Plant Biol

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Plant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution and enhanced adaptability. However, few studies have been conducted on the relationship between gene expression and epigenetic modification in different plant tissues after allopolyploidization. In this study, we studied gene expression and DNA methylation modification patterns in four tissues (stems, leaves, flowers and siliques) of Brassica napusand its diploid progenitors. On this basis, the alternative splicing patterns and cis-trans regulation patterns of four tissues in B. napus and its diploid progenitors were also analyzed. It can be seen that the number of alternative splicing occurs in the B. napus is higher than that in the diploid progenitors, and the IR type increases the most during allopolyploidy. In addition, we studied the fate changes of duplicated genes after allopolyploidization in B. napus. We found that the fate of most duplicated genes is conserved, but the number of neofunctionalization and specialization is also large. The genetic fate of B. napus was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study also analyzed generational transmission analysis of expression and DNA methylation patterns. Our study provides a reference for the fate differentiation of duplicated genes during allopolyploidization.

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Section: Introductionmentioning

confidence: 99%

Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus

Sun,

Li,

Wang

2024

BMC Plant Biol

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The genetic and molecular basis of haploinsufficiency in flowering plants

Navarro-Quiles,

Lup,

Muñoz-Nortes

et al. 2024

Trends in Plant Science

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Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data

DeGiorgio

Assis

2020

Molecular Biology and Evolution

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Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for functional divergence, and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the parameters driving duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built on a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents a major advancement in classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.

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Gene Dosage Balance Immediately following Whole-Genome Duplication in Arabidopsis

Cited by 4 publications

References 4 publications

Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus

Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus

The genetic and molecular basis of haploinsufficiency in flowering plants

Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data

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