Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics

Abstract The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels, resulting in the modern day cultivars. We studied the root growth of 3 different triploid banana cultivars under control and osmotic stress conditions. The root growth of the allopolyplo...

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Autores principales:	Jelle van Wesemael, Yann Hueber, Ewaut Kissel, Nádia Campos, Rony Swennen, Sebastien Carpentier
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/426b267b31e74935844af57a55d859af
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spelling	oai:doaj.org-article:426b267b31e74935844af57a55d859af2021-12-02T15:08:14ZHomeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics10.1038/s41598-018-19684-52045-2322https://doaj.org/article/426b267b31e74935844af57a55d859af2018-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-19684-5https://doaj.org/toc/2045-2322Abstract The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels, resulting in the modern day cultivars. We studied the root growth of 3 different triploid banana cultivars under control and osmotic stress conditions. The root growth of the allopolyploid ABB cultivar was 42% higher under control and 61% higher under osmotic stress. By integrating transcriptomics and proteomics, we studied the gene expression of all 3 cultivars, resulting in 2,749 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). In the ABB cultivar, allele expressions supposedly follow a 1/3 and 2/3 pattern for respectively the A and the B allele. Using transcriptome read alignment to assess the homeoallelic contribution we found that 63% of the allele specific genes deviated from this expectation. 32 gene loci even did not express the A allele. The identified ABB allele- specific proteins correlate well with the observed growth phenotype as they are enriched in energy related functions such as ATP metabolic processes, nicotinamide nucleotide metabolic processes, and glycolysis.Jelle van WesemaelYann HueberEwaut KisselNádia CamposRony SwennenSebastien CarpentierNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jelle van Wesemael Yann Hueber Ewaut Kissel Nádia Campos Rony Swennen Sebastien Carpentier Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
description	Abstract The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels, resulting in the modern day cultivars. We studied the root growth of 3 different triploid banana cultivars under control and osmotic stress conditions. The root growth of the allopolyploid ABB cultivar was 42% higher under control and 61% higher under osmotic stress. By integrating transcriptomics and proteomics, we studied the gene expression of all 3 cultivars, resulting in 2,749 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). In the ABB cultivar, allele expressions supposedly follow a 1/3 and 2/3 pattern for respectively the A and the B allele. Using transcriptome read alignment to assess the homeoallelic contribution we found that 63% of the allele specific genes deviated from this expectation. 32 gene loci even did not express the A allele. The identified ABB allele- specific proteins correlate well with the observed growth phenotype as they are enriched in energy related functions such as ATP metabolic processes, nicotinamide nucleotide metabolic processes, and glycolysis.
format	article
author	Jelle van Wesemael Yann Hueber Ewaut Kissel Nádia Campos Rony Swennen Sebastien Carpentier
author_facet	Jelle van Wesemael Yann Hueber Ewaut Kissel Nádia Campos Rony Swennen Sebastien Carpentier
author_sort	Jelle van Wesemael
title	Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
title_short	Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
title_full	Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
title_fullStr	Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
title_full_unstemmed	Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
title_sort	homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/426b267b31e74935844af57a55d859af
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Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics

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