Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum

Abstract Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diat...

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Autores principales:	Antoine Hoguin, Achal Rastogi, Chris Bowler, Leila Tirichine
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2440ff3fb72a4e8686531f02f20a603b
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spelling	oai:doaj.org-article:2440ff3fb72a4e8686531f02f20a603b2021-12-02T10:44:14ZGenome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum10.1038/s41598-021-82529-12045-2322https://doaj.org/article/2440ff3fb72a4e8686531f02f20a603b2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82529-1https://doaj.org/toc/2045-2322Abstract Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.Antoine HoguinAchal RastogiChris BowlerLeila TirichineNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Antoine Hoguin Achal Rastogi Chris Bowler Leila Tirichine Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum
description	Abstract Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.
format	article
author	Antoine Hoguin Achal Rastogi Chris Bowler Leila Tirichine
author_facet	Antoine Hoguin Achal Rastogi Chris Bowler Leila Tirichine
author_sort	Antoine Hoguin
title	Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum
title_short	Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum
title_full	Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum
title_fullStr	Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum
title_full_unstemmed	Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum
title_sort	genome-wide analysis of allele-specific expression of genes in the model diatom phaeodactylum tricornutum
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/2440ff3fb72a4e8686531f02f20a603b
work_keys_str_mv	AT antoinehoguin genomewideanalysisofallelespecificexpressionofgenesinthemodeldiatomphaeodactylumtricornutum AT achalrastogi genomewideanalysisofallelespecificexpressionofgenesinthemodeldiatomphaeodactylumtricornutum AT chrisbowler genomewideanalysisofallelespecificexpressionofgenesinthemodeldiatomphaeodactylumtricornutum AT leilatirichine genomewideanalysisofallelespecificexpressionofgenesinthemodeldiatomphaeodactylumtricornutum
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Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum

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