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(but not sufficient) to fully understand and consider its biology and its current and
future capabilities.
Prokaryotic Microalgae The most ubiquitous marine microalgae are the cyanobacteria, including the genera Prochlorococcus and Synechococcus. These are
found thriving throughout marine systems, including throughout vast nutrientlimited pelagic deserts where organic nitrogen, phosphorus, iron, or silicate are
insufficient for larger microalgae to thrive. The genomes of Prochlorococcus and
Synechococcus are approximately 1.5–2.5 Mbp in length and contain between 1000
and 2500 genes (Dufresne et al. 2003; Palenik et al. 2003; Rocap et al. 2003), typically including all of the genes necessary for photosynthesis. These genomes appear
remarkably streamlined in comparison to the 4.6Mbp genome of the E. coli bacterium, consisting of approximately 4300 genes (Blattner et al. 1997). It is hypothesized that the small genome sizes of cyanobacteria are optimized for nutrient-limited
environments (Bentkowski et al. 2017).
Eukaryotic Microalgae The first fully sequenced marine microeukaryote genomes
have revealed a surprising genetic and physiological complexity hidden within
seemingly simple unicellular plankton. The genome of the siliceous “cosmopolitan”
diatom, Thalassiosira pseudonana, the first diatom sequenced due to its ubiquity
and compact genome size (32 Mbp), consists of 24 chromosomes and encodes an
estimated 11,390 genes (Armbrust et al. 2004). Roughly half of these genes bear no
confident similarity to any other genes of known function. The genome of
Phaeodactylum tricornutum, the second diatom to be sequenced, similarly encodes
over 10,000 genes, only about half of which bear detectable similarity to those
found in T. pseudonana, despite only ~90 million years of divergent evolution
between the two species. Both of these marine microeukaryote genomes imply a
complexity greater than that of the first fully sequenced microeukaryote, the yeast
Saccharomyces cerevisiae, the 12 Mbp genome of which consists of ~6000 genes
(Goffeau et al. 1996). Similarly, the ~120 Mbp genome of the freshwater microalga
Chlamydomonas reinhardtii harbors a surprisingly complex genome encoding
~16,700 genes (Merchant et al. 2007), less than 3000 of whose products bear confident similarity to those encoded in the genomes of T. pseudonana (Armbrust et al.
2004) or P. tricornutum (Bowler et al. 2008). The collection of microalgal genomes
is rapidly expanding, including several additional diatom (Lommer et al. 2012;
Traller et al. 2016; Mock et al. 2017; Basu et al. 2017) and dinoflagellate (Lin et al.
2015) genomes now available for research into these lesser understood phyla. In
addition to this, at least hundreds of new genomes and millions of new putative
protein coding genes have been cataloged by the latest exploratory and integrative
oceanographic efforts (de Vargas et al. 2015).
Marine Microbial Metagenomes Within any water sample or marine ecosystem,
there are multiple genomes present, numbering from the tens to trillions, depending
on scale. The specific repertoires of variously encoded functions and alleles in any
sample define the genetic potential of biological processes in that context and specify salient functions and features that are adapted to exist in the environment from
10 Marine Microalgae: Systems Biology from ‘Omics
(but not sufficient) to fully understand and consider its biology and its current and
future capabilities.
Prokaryotic Microalgae The most ubiquitous marine microalgae are the cyanobacteria, including the genera Prochlorococcus and Synechococcus. These are
found thriving throughout marine systems, including throughout vast nutrientlimited pelagic deserts where organic nitrogen, phosphorus, iron, or silicate are
insufficient for larger microalgae to thrive. The genomes of Prochlorococcus and
Synechococcus are approximately 1.5–2.5 Mbp in length and contain between 1000
and 2500 genes (Dufresne et al. 2003; Palenik et al. 2003; Rocap et al. 2003), typically including all of the genes necessary for photosynthesis. These genomes appear
remarkably streamlined in comparison to the 4.6Mbp genome of the E. coli bacterium, consisting of approximately 4300 genes (Blattner et al. 1997). It is hypothesized that the small genome sizes of cyanobacteria are optimized for nutrient-limited
environments (Bentkowski et al. 2017).
Eukaryotic Microalgae The first fully sequenced marine microeukaryote genomes
have revealed a surprising genetic and physiological complexity hidden within
seemingly simple unicellular plankton. The genome of the siliceous “cosmopolitan”
diatom, Thalassiosira pseudonana, the first diatom sequenced due to its ubiquity
and compact genome size (32 Mbp), consists of 24 chromosomes and encodes an
estimated 11,390 genes (Armbrust et al. 2004). Roughly half of these genes bear no
confident similarity to any other genes of known function. The genome of
Phaeodactylum tricornutum, the second diatom to be sequenced, similarly encodes
over 10,000 genes, only about half of which bear detectable similarity to those
found in T. pseudonana, despite only ~90 million years of divergent evolution
between the two species. Both of these marine microeukaryote genomes imply a
complexity greater than that of the first fully sequenced microeukaryote, the yeast
Saccharomyces cerevisiae, the 12 Mbp genome of which consists of ~6000 genes
(Goffeau et al. 1996). Similarly, the ~120 Mbp genome of the freshwater microalga
Chlamydomonas reinhardtii harbors a surprisingly complex genome encoding
~16,700 genes (Merchant et al. 2007), less than 3000 of whose products bear confident similarity to those encoded in the genomes of T. pseudonana (Armbrust et al.
2004) or P. tricornutum (Bowler et al. 2008). The collection of microalgal genomes
is rapidly expanding, including several additional diatom (Lommer et al. 2012;
Traller et al. 2016; Mock et al. 2017; Basu et al. 2017) and dinoflagellate (Lin et al.
2015) genomes now available for research into these lesser understood phyla. In
addition to this, at least hundreds of new genomes and millions of new putative
protein coding genes have been cataloged by the latest exploratory and integrative
oceanographic efforts (de Vargas et al. 2015).
Marine Microbial Metagenomes Within any water sample or marine ecosystem,
there are multiple genomes present, numbering from the tens to trillions, depending
on scale. The specific repertoires of variously encoded functions and alleles in any
sample define the genetic potential of biological processes in that context and specify salient functions and features that are adapted to exist in the environment from
10 Marine Microalgae: Systems Biology from ‘Omics