212
which the sample was collected. The genomic information typically observed in
marine environments is inexhaustibly complex and difficult to assemble or reduce
(Gilbert and Dupont 2011; Iverson et al. 2012). Nevertheless, the sample-specific
richness of taxonomy, diversity, allele distribution, and function gained through
high-depth short-read sequencing of environmental samples quickly yields critical
information to understand the aggregate nature and properties of marine microbial
systems (Venter et al. 2004; Sunagawa et al. 2015). The genome, however, is largely
passive and inactive and merely a source code in all living systems. In order to
understand how the information stored and transmitted in genomes relates to
biology itself, it is necessary to consider the messages and biomolecules transcribed
from genomes to perform cellular functions.
10.4 Marine Microalgal Transcriptomics
The primary (and likely most ancient) dynamically encoded information in the cell
is contained within RNAs conditionally and flexibly transcribed to and from the
functionally inactive genome. Fortunately, this is also now relatively comprehensive
and easy information to obtain through high-throughput sequencing. For microeukaryotes with large genome sizes and mixed cultures or in environmental samples,
the size and complexity of the expressed transcriptome are significantly smaller in
size than the corresponding whole genome space and by definition contain nearly
all of genetically encoded functional information that is operating under a particular
condition. These information, which are in many cases now readily comprehensive,
provide a wealth of detailed information about crucially acting molecular processes
and the emergent patterns of gene expression that give rise to various cellular states.
While it is necessary but not sufficient to explain the operation of biological systems, transcriptomic data currently represent the broadest, most sensitive, and most
easily obtainable and intercomparable system-wide functional information that can
be collected for most organisms and biological systems.
The putative biological activities of the proteins produced by typically about half
of all microalgal transcripts can be inferred bioinformatically, and while in some
examples and species the expression levels of proteins can be uncorrelated to the
expression levels of their transcripts, increases or decreases of mRNA transcript
levels are often concordant with changes in the cellular levels of the proteins that
they encode. mRNA sequencing of genetically variable species or environments
also yields nucleotide polymorphisms in conserved and evolutionarily pressured
protein-coding regions that may be linked to spatial, temporal, ecological, evolutionary, and functional divergence. For all of these reasons, a wealth of transcriptomic and metatranscriptomic data has been collected for marine microalgal species
in a very short time. These data can be used to rapidly characterize informative gene
regulatory profiles of biological systems in accordance with varying cellular states
and environments.
J. Ashworth
which the sample was collected. The genomic information typically observed in
marine environments is inexhaustibly complex and difficult to assemble or reduce
(Gilbert and Dupont 2011; Iverson et al. 2012). Nevertheless, the sample-specific
richness of taxonomy, diversity, allele distribution, and function gained through
high-depth short-read sequencing of environmental samples quickly yields critical
information to understand the aggregate nature and properties of marine microbial
systems (Venter et al. 2004; Sunagawa et al. 2015). The genome, however, is largely
passive and inactive and merely a source code in all living systems. In order to
understand how the information stored and transmitted in genomes relates to
biology itself, it is necessary to consider the messages and biomolecules transcribed
from genomes to perform cellular functions.
10.4 Marine Microalgal Transcriptomics
The primary (and likely most ancient) dynamically encoded information in the cell
is contained within RNAs conditionally and flexibly transcribed to and from the
functionally inactive genome. Fortunately, this is also now relatively comprehensive
and easy information to obtain through high-throughput sequencing. For microeukaryotes with large genome sizes and mixed cultures or in environmental samples,
the size and complexity of the expressed transcriptome are significantly smaller in
size than the corresponding whole genome space and by definition contain nearly
all of genetically encoded functional information that is operating under a particular
condition. These information, which are in many cases now readily comprehensive,
provide a wealth of detailed information about crucially acting molecular processes
and the emergent patterns of gene expression that give rise to various cellular states.
While it is necessary but not sufficient to explain the operation of biological systems, transcriptomic data currently represent the broadest, most sensitive, and most
easily obtainable and intercomparable system-wide functional information that can
be collected for most organisms and biological systems.
The putative biological activities of the proteins produced by typically about half
of all microalgal transcripts can be inferred bioinformatically, and while in some
examples and species the expression levels of proteins can be uncorrelated to the
expression levels of their transcripts, increases or decreases of mRNA transcript
levels are often concordant with changes in the cellular levels of the proteins that
they encode. mRNA sequencing of genetically variable species or environments
also yields nucleotide polymorphisms in conserved and evolutionarily pressured
protein-coding regions that may be linked to spatial, temporal, ecological, evolutionary, and functional divergence. For all of these reasons, a wealth of transcriptomic and metatranscriptomic data has been collected for marine microalgal species
in a very short time. These data can be used to rapidly characterize informative gene
regulatory profiles of biological systems in accordance with varying cellular states
and environments.
J. Ashworth