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Divergence of duplicated genes by repeated partitioning of splice forms and subcellular localization

Qiu, Yichun and Tay, Yii Van and Ruan, Yuan and Adams, Keith L. (2020) Divergence of duplicated genes by repeated partitioning of splice forms and subcellular localization. New Phytologist, 225 (2). pp. 1011-1022. ISSN 0028-646X. https://resolver.caltech.edu/CaltechAUTHORS:20190910-132622483

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Abstract

Gene duplication is a prominent and recurrent process in plant genomes. Among the possible fates of duplicated genes, subfunctionalization refers to duplicates taking on different parts of the function or expression pattern of the ancestral gene. This partitioning could be accompanied by changes in subcellular localization of the protein products. We propose that when alternative splicing of gene products leads to protein products with different subcellular localizations, after gene duplication there will be partitioning of the alternatively spliced forms such that the products of each duplicate are localized to only one of the original locations which we refer to as sub‐localization. We identified the plastid ascorbate peroxidase (cpAPX) genes across angiosperms and analyzed their duplication history, alternative splicing, and subcellular targeting patterns, to identify cases of sub‐localization. We found angiosperms typically have one cpAPX gene that generates both thylakoidal APX (tAPX) and stromal APX (sAPX) through alternative splicing. We identified several independent lineage‐specific sub‐localization cases with specialized paralogs of tAPX and sAPX. We determined that the sub‐localization happened through two types of sequence evolution patterns. Our findings suggest that the divergence through sub‐localization is key to the retention of paralogous cpAPX genes in angiosperms.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1111/nph.16148DOIArticle
Additional Information:© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust. Issue Online: 19 December 2019; Version of Record online: 03 October 2019; Accepted manuscript online: 30 August 2019; Manuscript accepted: 21 August 2019; Manuscript received: 30 June 2019. Funding Information: Natural Science and Engineering Research Council of Canada.
Funders:
Funding AgencyGrant Number
Natural Science and Engineering Research Council of Canada (NSERC)UNSPECIFIED
Subject Keywords:alternative splicing; gene duplication; plastid ascorbate peroxidase; subcellular localization; sublocalization
Issue or Number:2
Record Number:CaltechAUTHORS:20190910-132622483
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190910-132622483
Official Citation:Qiu, Y., Tay, Y.V., Ruan, Y. and Adams, K.L. (2020), Divergence of duplicated genes by repeated partitioning of splice forms and subcellular localization. New Phytol, 225: 1011-1022. doi:10.1111/nph.16148
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:98556
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Sep 2019 20:46
Last Modified:02 Jan 2020 20:58

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