Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina

Abstract Despite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) b...

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Autores principales:	Bahman Panahi, Mohammad Amin Hejazi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7962ccc3234d4c789eba3032e7d0cdca
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spelling	oai:doaj.org-article:7962ccc3234d4c789eba3032e7d0cdca2021-12-02T15:23:09ZWeighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina10.1038/s41598-020-80945-32045-2322https://doaj.org/article/7962ccc3234d4c789eba3032e7d0cdca2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80945-3https://doaj.org/toc/2045-2322Abstract Despite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) between hypersaline and normal conditions. Then, using weighted gene co-expression network analysis (WGCNA), which takes advantage of a graph theoretical approach, highly correlated genes were clustered as a module. Subsequently, connectivity patterns of the identified modules in two conditions were surveyed to define preserved and non-preserved modules by combining the Zsummary and medianRank measures. Finally, common and specific hub genes in non-preserved modules were determined using Eigengene-based module connectivity or module membership (kME) measures and validation was performed by using leave-one-out cross-validation (LOOCV). In this study, the power of beta = 12 (scale-free R2 = 0.8) was selected as the soft-thresholding to ensure a scale-free network, which led to the identification of 15 co-expression modules. Results also indicate that green, blue, brown, and yellow modules are non-preserved in salinity stress conditions. Examples of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in non-preserved modules are Sulfur metabolism, Oxidative phosphorylation, Porphyrin and chlorophyll metabolism, Vitamin B6 metabolism. Moreover, the systems biology approach was applied here, proposed some salinity specific hub genes, such as radical-induced cell death1 protein (RCD1), mitogen-activated protein kinase kinase kinase 13 (MAP3K13), long-chain acyl-CoA synthetase (ACSL), acetyl-CoA carboxylase, biotin carboxylase subunit (AccC), and fructose-bisphosphate aldolase (ALDO), for the development of metabolites accumulating strains in D. salina.Bahman PanahiMohammad Amin HejaziNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bahman Panahi Mohammad Amin Hejazi Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina
description	Abstract Despite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) between hypersaline and normal conditions. Then, using weighted gene co-expression network analysis (WGCNA), which takes advantage of a graph theoretical approach, highly correlated genes were clustered as a module. Subsequently, connectivity patterns of the identified modules in two conditions were surveyed to define preserved and non-preserved modules by combining the Zsummary and medianRank measures. Finally, common and specific hub genes in non-preserved modules were determined using Eigengene-based module connectivity or module membership (kME) measures and validation was performed by using leave-one-out cross-validation (LOOCV). In this study, the power of beta = 12 (scale-free R2 = 0.8) was selected as the soft-thresholding to ensure a scale-free network, which led to the identification of 15 co-expression modules. Results also indicate that green, blue, brown, and yellow modules are non-preserved in salinity stress conditions. Examples of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in non-preserved modules are Sulfur metabolism, Oxidative phosphorylation, Porphyrin and chlorophyll metabolism, Vitamin B6 metabolism. Moreover, the systems biology approach was applied here, proposed some salinity specific hub genes, such as radical-induced cell death1 protein (RCD1), mitogen-activated protein kinase kinase kinase 13 (MAP3K13), long-chain acyl-CoA synthetase (ACSL), acetyl-CoA carboxylase, biotin carboxylase subunit (AccC), and fructose-bisphosphate aldolase (ALDO), for the development of metabolites accumulating strains in D. salina.
format	article
author	Bahman Panahi Mohammad Amin Hejazi
author_facet	Bahman Panahi Mohammad Amin Hejazi
author_sort	Bahman Panahi
title	Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina
title_short	Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina
title_full	Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina
title_fullStr	Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina
title_full_unstemmed	Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina
title_sort	weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae dunaliella salina
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/7962ccc3234d4c789eba3032e7d0cdca
work_keys_str_mv	AT bahmanpanahi weightedgenecoexpressionnetworkanalysisofthesaltresponsivetranscriptomesrevealsnovelhubgenesingreenhalophyticmicroalgaedunaliellasalina AT mohammadaminhejazi weightedgenecoexpressionnetworkanalysisofthesaltresponsivetranscriptomesrevealsnovelhubgenesingreenhalophyticmicroalgaedunaliellasalina
_version_	1718387332939251712

Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina

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