S2E9 | Sunil Kenchanmane Raju | DNA methylation and Gene duplication

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No Time To Read

Arif Ashraf

30 episodes

2 weeks ago

Arif, plant biologist and host of the podcast, will talk to lead author of a recently published plant biology paper. The guest will simply explain the story of the publication, answer questions from the host, and share personal experience and details related to the article. As an audience, you will tune in to the episode with an expectation that you will know the story of the paper without reading it. Besides, you can keep listening the podcast during your experiment, walking outside, in your car and wherever possible.

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S2E9 | Sunil Kenchanmane Raju | DNA methylation and Gene duplication

No Time To Read

32 minutes 5 seconds

2 years ago

S2E9 | Sunil Kenchanmane Raju | DNA methylation and Gene duplication

Article: DNA methylation signatures of duplicate gene evolution in angiosperms

Journal: Plant Physiology

Year: 2023

Guest: Sunil Kenchanmane Raju

Host: Arif Ashraf

Abstract

Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomic approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole-genome duplicates were typically enriched for CG-only gene body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was a characteristic of more recent single-gene duplicates. Core angiosperm gene families were differentiated into those which preferentially retain paralogs and “duplication-resistant” families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence–absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.

Cover art design and audio editing: Ragib Anjum