152
a significant role as a central carbon and energy metabolisms process, it is clearly
important to investigate not only photobiology but also the connected metabolic
pathways in order to predict seagrass responses to environmental changes effectively. With high-throughput experiments being increasingly common, combining
the “omics” approaches can help us to gain a systemic understanding of photosynthesis within plant complex metabolic networks. Although being in its early stage,
many seagrass scientists have pioneered research in this field (Reusch et al. 2008;
Franssen et al. 2011; Winters et al. 2011; Dattolo et al. 2013, 2014; Mazzuca et al.
2013; Piro et al. 2015a, b; Kumar et al. 2016a). It is only recently that the first
genomic data has become available from Z. marina, a common seagrass species of
the northern hemisphere (Olsen et al. 2016) followed by its relative from the southern hemisphere, Z. muelleri (Lee et al. 2016). The availability of full genome
sequences for these species means that we can now adopt a systems approach to
investigate the metabolic networks of these seagrasses and how environmental
changes modulate their metabolisms. Detailed reviews of the utilization of omics
techniques and molecular profiling in seagrass studies in the past decade and concepts and applications of metabolomics in the marine macrophytes studies have
been recently presented by Davey et al. (2016) and Kumar et al. (2016b), respectively. Here, omics approaches are briefly described. Further, examples of omics
investigations in model photosynthetic organisms which can be adopted to address
the knowledge gaps related to seagrass photobiology are discussed.
Transcriptomics and proteomics analyses have been proven to provide a good
systemic overview in seagrass metabolisms. The number of transcriptomic and proteomic studies carried out in seagrass is growing (Franssen et al. 2011; Winters et al.
2011; Dattolo et al. 2013, 2014; Mazzuca et al. 2013; Piro et al. 2015a, b; Kumar
et al. 2016a). In these works, stressors were applied to seagrasses to unravel the
underlying metabolic pathways which are involved in stress responses or tolerance.
Comparative transcriptomics and proteomics focus on differential gene and protein
expression levels of the entire transcriptome and proteome induced by environmental
changes (Franssen et al. 2011; Winters et al. 2011; Dattolo et al. 2013, 2014; Mazzuca
et al. 2013; Piro et al. 2015a, b; Kumar et al. 2016a). Transcripts and proteins differentially expressed due to the environmental stimuli such as high temperature,
salinity, and light gradient have been identified, as well as the metabolic pathway
they are part of. Metabolomics is another new frontier in plant systems biology. It
greatly complements transcriptome and proteome analysis as the difference in quality and quantity of metabolites readily reflect cellular biochemical processes.
Metabolome analysis provides comprehensive and dynamic views of plant primary
and secondary metabolites under changing environments. Although remained unexplored in seagrasses, it holds great potential for seagrass research (see extended
review by Kumar et al. 2016b).
To better understand the photosynthetic mechanisms and interconnectivity
between photosynthesis and other metabolic pathways of seagrasses, it is crucial to
conduct a parallel analysis of transcript, protein, and metabolic profiles. Combined
omics data have provided valuable insights into mechanisms of carbon acquisition
and accumulation in the green alga, Chlamydomonas reinhardtii (reviewed in Winck
P. Buapet
a significant role as a central carbon and energy metabolisms process, it is clearly
important to investigate not only photobiology but also the connected metabolic
pathways in order to predict seagrass responses to environmental changes effectively. With high-throughput experiments being increasingly common, combining
the “omics” approaches can help us to gain a systemic understanding of photosynthesis within plant complex metabolic networks. Although being in its early stage,
many seagrass scientists have pioneered research in this field (Reusch et al. 2008;
Franssen et al. 2011; Winters et al. 2011; Dattolo et al. 2013, 2014; Mazzuca et al.
2013; Piro et al. 2015a, b; Kumar et al. 2016a). It is only recently that the first
genomic data has become available from Z. marina, a common seagrass species of
the northern hemisphere (Olsen et al. 2016) followed by its relative from the southern hemisphere, Z. muelleri (Lee et al. 2016). The availability of full genome
sequences for these species means that we can now adopt a systems approach to
investigate the metabolic networks of these seagrasses and how environmental
changes modulate their metabolisms. Detailed reviews of the utilization of omics
techniques and molecular profiling in seagrass studies in the past decade and concepts and applications of metabolomics in the marine macrophytes studies have
been recently presented by Davey et al. (2016) and Kumar et al. (2016b), respectively. Here, omics approaches are briefly described. Further, examples of omics
investigations in model photosynthetic organisms which can be adopted to address
the knowledge gaps related to seagrass photobiology are discussed.
Transcriptomics and proteomics analyses have been proven to provide a good
systemic overview in seagrass metabolisms. The number of transcriptomic and proteomic studies carried out in seagrass is growing (Franssen et al. 2011; Winters et al.
2011; Dattolo et al. 2013, 2014; Mazzuca et al. 2013; Piro et al. 2015a, b; Kumar
et al. 2016a). In these works, stressors were applied to seagrasses to unravel the
underlying metabolic pathways which are involved in stress responses or tolerance.
Comparative transcriptomics and proteomics focus on differential gene and protein
expression levels of the entire transcriptome and proteome induced by environmental
changes (Franssen et al. 2011; Winters et al. 2011; Dattolo et al. 2013, 2014; Mazzuca
et al. 2013; Piro et al. 2015a, b; Kumar et al. 2016a). Transcripts and proteins differentially expressed due to the environmental stimuli such as high temperature,
salinity, and light gradient have been identified, as well as the metabolic pathway
they are part of. Metabolomics is another new frontier in plant systems biology. It
greatly complements transcriptome and proteome analysis as the difference in quality and quantity of metabolites readily reflect cellular biochemical processes.
Metabolome analysis provides comprehensive and dynamic views of plant primary
and secondary metabolites under changing environments. Although remained unexplored in seagrasses, it holds great potential for seagrass research (see extended
review by Kumar et al. 2016b).
To better understand the photosynthetic mechanisms and interconnectivity
between photosynthesis and other metabolic pathways of seagrasses, it is crucial to
conduct a parallel analysis of transcript, protein, and metabolic profiles. Combined
omics data have provided valuable insights into mechanisms of carbon acquisition
and accumulation in the green alga, Chlamydomonas reinhardtii (reviewed in Winck
P. Buapet