Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum

Ashworth, J; Turkarslan, S; Harris, M; Orellana, MV; Baliga, NS

Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum

Ashworth, J

Turkarslan, S Harris, M Orellana, MV Baliga, NS

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Publication Type:: Journal Article
Citation:: Marine Genomics, 2016, 26 pp. 21 - 28
Issue Date:: 2016-04-01

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Field	Value	Language
dc.contributor.author	Ashworth, J https://orcid.org/0000-0003-4835-6551	en_US
dc.contributor.author	Turkarslan, S	en_US
dc.contributor.author	Harris, M	en_US
dc.contributor.author	Orellana, MV	en_US
dc.contributor.author	Baliga, NS	en_US
dc.date.available	2015-10-29	en_US
dc.date.issued	2016-04-01	en_US
dc.identifier.citation	Marine Genomics, 2016, 26 pp. 21 - 28	en_US
dc.identifier.issn	1874-7787	en_US
dc.identifier.uri	http://hdl.handle.net/10453/122771
dc.description.abstract	© 2015 Elsevier B.V. Diatoms are important primary producers in the ocean that thrive in diverse and dynamic environments. Their survival and success over changing conditions depend on the complex coordination of gene regulatory processes. Here we present an integrated analysis of all publicly available microarray data for the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. This resource includes shared expression patterns, gene functions, and cis-regulatory DNA sequence motifs in each species that are statistically coordinated over many experiments. These data illustrate the coordination of transcriptional responses in diatoms over changing environmental conditions. Responses to silicic acid depletion segregate into multiple distinctly regulated groups of genes, regulation by heat shock transcription factors (HSFs) is implicated in the response to nitrate stress, and distinctly coordinated carbon concentrating, CO2 and pH-related responses are apparent. Fundamental features of diatom physiology are similarly coordinated between two distantly related diatom species, including the regulation of photosynthesis, cellular growth functions and lipid metabolism. These integrated data and analyses can be explored publicly (http://networks.systemsbiology.net/diatom-portal/).	en_US
dc.relation.ispartof	Marine Genomics	en_US
dc.relation.isbasedon	10.1016/j.margen.2015.10.011	en_US
dc.subject.mesh	Diatoms	en_US
dc.subject.mesh	Cluster Analysis	en_US
dc.subject.mesh	Phylogeny	en_US
dc.subject.mesh	Gene Expression Regulation	en_US
dc.subject.mesh	Transcriptome	en_US
dc.title	Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum	en_US
dc.type	Journal Article
utslib.citation.volume	26	en_US
utslib.for	0602 Ecology	en_US
utslib.for	0604 Genetics	en_US
utslib.for	06 Biological Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	closed_access
pubs.publication-status	Published	en_US
pubs.volume	26	en_US

Abstract:

© 2015 Elsevier B.V. Diatoms are important primary producers in the ocean that thrive in diverse and dynamic environments. Their survival and success over changing conditions depend on the complex coordination of gene regulatory processes. Here we present an integrated analysis of all publicly available microarray data for the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. This resource includes shared expression patterns, gene functions, and cis-regulatory DNA sequence motifs in each species that are statistically coordinated over many experiments. These data illustrate the coordination of transcriptional responses in diatoms over changing environmental conditions. Responses to silicic acid depletion segregate into multiple distinctly regulated groups of genes, regulation by heat shock transcription factors (HSFs) is implicated in the response to nitrate stress, and distinctly coordinated carbon concentrating, CO2 and pH-related responses are apparent. Fundamental features of diatom physiology are similarly coordinated between two distantly related diatom species, including the regulation of photosynthesis, cellular growth functions and lipid metabolism. These integrated data and analyses can be explored publicly (http://networks.systemsbiology.net/diatom-portal/).

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http://hdl.handle.net/10453/122771