Biomedical Engineering Reference
In-Depth Information
the extracellular frustule via obligate dependence upon silicon in the environment
[ 23 ]. The P. tricornutum and T. pseudonana genomes allowed the identification of
genes involved in silica nanofabrication in both diatoms. Moreover, variation and
dynamics of gene expression in P. tricornutum under different Si levels unraveled
the transportation and metabolism pathways of silicon as well as the associated
transcriptional and post-transcriptional regulatory mechanism [ 25 ]. In oleaginous
algae such as Nannochloropsis, the genomes are expected to reveal the diversity of
the structural and regulatory genes and pathways that underlie robust lipid pro-
duction. Such sequences can serve as novel phylogenetic markers or functional
markers for strain-typing oleaginous microalgae, for which reliable and sensitive
identification and tracking of strains have been non-trivial due to the absence of
easily distinguishable morphological features in these single-cell organisms. These
markers, once validated and tested over a broader range of isolates, might enable a
genotyping-based strategy for strain characterization, which can be of much higher
throughput than the traditional phenotyping-based selection strategies, and thus
might change the paradigm of microalgal feedstock screening and selection.
(2) Evolution of functional elements underlying the key traits of oleaginous
algae. In O. tauri and O. lucimarinus, chromosomes 19 and 18, respectively, were
hypothesized to be exogenously acquired after the divergence of the two species
because they exhibited different GC contents and distinct codon usage from the
core genomes and harbored genes that were either unknown or more similar to
bacteria than green algae (such as those altering the cell-surface glycosylation as a
defense mechanism to the marine environment [ 21 ]). The P. tricornutum genome
also comprised hundreds of genes horizontally transferred from bacteria [ 24 ].
These findings suggested that horizontal gene transfer contributed to the origin of
microalgal genetic variation, leading to the creation of new genes and new gene
functions [ 26 ]. In oleaginous microalgae, a number of important hypotheses
regarding the origin and evolution of functional elements, particularly those related
to the key traits, can be tested via their genome sequences, such as pan-genome or
phylo-genome. For example, what are the genomic definitions of genus, species
and strains? Is there a core genome shared by a group of phylogenetically closely
related strains? How large are the cores? Do the cores and the accessories encode a
similar set of functions or evolve in a similar manner? Are the key traits important
to robust lipid production found at the core or at the accessories? Are different
functions evolving at distinguishable rates or of different origin? Are the single-
cell organisms such as microalgae evolving at a different rate from their multi-
cellular relatives? Moreover, as microalgae inevitably encounter a plethora of
environmental ''shocks'' or ''stresses'' during an outdoor cultivation process, it
would be essential to understand the significance and nature of microevolution in
genome structure and function. Key questions include the links between genotype
evolution and phenotype alteration, the potential difference between coding
sequence evolution versus non-coding sequence evolution, and the distinction
between structural gene evolution versus regulatory gene evolution. These ques-
tions will shed light on rational strategies and practices for engineering favorable
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