213
Laboratory Studies The first comprehensive genome-wide expression studies in
marine microalgae consisted of single-species experiments in which wholetranscriptome microarrays were used to measure changes in the expression of all
genes under various conditions of relevance to the natural environment. These
include tracking the cyanobacterium Prochlorococcus over its day/night cycle
(Waldbauer et al. 2012), measuring the comprehensive responses of the diatom T.
pseudonana to a panel of typical stresses and limitations (Mock et al. 2008), and
interacting factors of the diel cycle, culture density, and nutrient exhaustion
(Ashworth et al. 2013). For the diatoms in particular, abundant transcriptome-wide
expression data have been collected using microarrays and mRNA sequencing
under various laboratory conditions designed to simulate environmental variables.
These include, among others: (1) T. pseudonana: silica, iron, and nitrogen limitation, low temperature and elevated pH (Mock et al. 2008), iron starvation
(Thamatrakoln et al. 2012), silica starvation and re-supplementation (Shrestha et al.
2012; Smith et al. 2016b), diel growth from exponential to stationary phase
(Ashworth et al. 2013), exposure to the pollutant benzo[a]pyrene (Carvalho et al.
2011), and growth at moderate and elevated CO 2 levels under moderate and elevated
light and (2) P. tricornutum: silica limitation (Sapriel et al. 2009), acclimation to
high light (Nymark et al. 2009), exposure to cadmium (Brembu et al. 2011), acclimation to light and dark cycles (Chauton et al. 2013), exposure to a panel of stresses
and pollutants (Hook and Osborn 2012), darkness and re-illumination (Nymark
et al. 2013), and growth in red, blue, and green light (Valle et al. 2014).
The comprehensive tracking of changes in gene expression over all of these various experimental conditions results in a rich and complex picture of transcriptome
dynamics in these organisms (Ashworth et al. 2013, 2016; Levering et al. 2017),
much of which is still yet to be sufficiently studied, understood, and fully applied to
address fundamental questions and predictions with regard to marine systems and
future change.
RNA Sequencing Whole transcriptome RNA sequencing at high depth has become
affordable enough to simplify the process and information necessary to obtain transcriptomic profiles for any species or biological sample. The sequencing of transcribed RNA repertoires through reverse transcription and amplification is powerful
and sensitive and can be informatively classified, quantified, and assembled even in
the absence of corresponding genome sequences. For eukaryotes in particular, the
functional and phylogenetic information density present in transcribed messenger
RNA is high, and the amplification of cDNA improves signal detection—particularly in the case of poly-dT-primed strand synthesis and 3′-directed selective amplification (Xiong et al. 2017). Laboratory mRNA sequencing studies in marine
microalgae include the profiling of diatoms to transcriptome dynamics at different
levels of carbon dioxide (Hennon et al. 2015), during silica starvation (Smith et al.
2016b), diel cycling combined with iron limitation (Smith et al. 2016a), and an
integrated range of several other environmental, nutrient, and chemical perturbations (Levering et al. 2017). Hundreds of additional new single-strain transcriptomes have been sequenced in order to cover dozens of completely new clades of
10 Marine Microalgae: Systems Biology from ‘Omics’
Laboratory Studies The first comprehensive genome-wide expression studies in
marine microalgae consisted of single-species experiments in which wholetranscriptome microarrays were used to measure changes in the expression of all
genes under various conditions of relevance to the natural environment. These
include tracking the cyanobacterium Prochlorococcus over its day/night cycle
(Waldbauer et al. 2012), measuring the comprehensive responses of the diatom T.
pseudonana to a panel of typical stresses and limitations (Mock et al. 2008), and
interacting factors of the diel cycle, culture density, and nutrient exhaustion
(Ashworth et al. 2013). For the diatoms in particular, abundant transcriptome-wide
expression data have been collected using microarrays and mRNA sequencing
under various laboratory conditions designed to simulate environmental variables.
These include, among others: (1) T. pseudonana: silica, iron, and nitrogen limitation, low temperature and elevated pH (Mock et al. 2008), iron starvation
(Thamatrakoln et al. 2012), silica starvation and re-supplementation (Shrestha et al.
2012; Smith et al. 2016b), diel growth from exponential to stationary phase
(Ashworth et al. 2013), exposure to the pollutant benzo[a]pyrene (Carvalho et al.
2011), and growth at moderate and elevated CO 2 levels under moderate and elevated
light and (2) P. tricornutum: silica limitation (Sapriel et al. 2009), acclimation to
high light (Nymark et al. 2009), exposure to cadmium (Brembu et al. 2011), acclimation to light and dark cycles (Chauton et al. 2013), exposure to a panel of stresses
and pollutants (Hook and Osborn 2012), darkness and re-illumination (Nymark
et al. 2013), and growth in red, blue, and green light (Valle et al. 2014).
The comprehensive tracking of changes in gene expression over all of these various experimental conditions results in a rich and complex picture of transcriptome
dynamics in these organisms (Ashworth et al. 2013, 2016; Levering et al. 2017),
much of which is still yet to be sufficiently studied, understood, and fully applied to
address fundamental questions and predictions with regard to marine systems and
future change.
RNA Sequencing Whole transcriptome RNA sequencing at high depth has become
affordable enough to simplify the process and information necessary to obtain transcriptomic profiles for any species or biological sample. The sequencing of transcribed RNA repertoires through reverse transcription and amplification is powerful
and sensitive and can be informatively classified, quantified, and assembled even in
the absence of corresponding genome sequences. For eukaryotes in particular, the
functional and phylogenetic information density present in transcribed messenger
RNA is high, and the amplification of cDNA improves signal detection—particularly in the case of poly-dT-primed strand synthesis and 3′-directed selective amplification (Xiong et al. 2017). Laboratory mRNA sequencing studies in marine
microalgae include the profiling of diatoms to transcriptome dynamics at different
levels of carbon dioxide (Hennon et al. 2015), during silica starvation (Smith et al.
2016b), diel cycling combined with iron limitation (Smith et al. 2016a), and an
integrated range of several other environmental, nutrient, and chemical perturbations (Levering et al. 2017). Hundreds of additional new single-strain transcriptomes have been sequenced in order to cover dozens of completely new clades of
10 Marine Microalgae: Systems Biology from ‘Omics’