6
Though whole genome sequence studies explored some uncommon genomic
features related to primary and secondary metabolism in seaweeds, the large part of
the genomic information remained unannotated. Independent transcriptomics studies with de novo assembly and annotation of data define the regulations seaweed
possess for habiting the coastal environmental conditions. For example, the transcriptome for Ulva linza revealed the existence of land-specific genes, special photoprotective mechanism based on both LhcSR and PsbS, evidence of C4-like
carbon-concentrating mechanisms, multi-origin transporters for essential inorganic
nutrients, multiple and complex P450s for its colonization on coastal waters and
bloom formation (Zhang et al. 2012). A few more transcriptomic studies further
advance our knowledge towards the physiology and regulations in Sargassum (Liu
et al. 2014), Pyropia (Im et al. 2015) and Undaria (Shan et al. 2015). These studies
have revealed a few unknown pathways and highlighted the existence of specialized
mechanisms in seaweeds, which are quite distinct from terrestrial counterparts.
However, more than 40% of transcriptomic information generated from these studies remained unassigned as there is no BLAST hit for those regions. Thus unique
regulatory elements of seaweeds either at functional or physiological aspects could
not be defined. Missing such valuable information is a major setback towards understanding of seaweed unique physiology and functioning. Thus, integration of datasets from functional and comparative genomics is mandatory which can generate a
more accurate and holistic view of genes of unknown function (Xu et al. 2014). A
few studies have been carried out to understand the metabolic processes in response
to salinity and oxidative stress in a brown alga and were correlated with transcriptome data (Gravot et al. 2010; Dittami et al. 2011; Konotchick et al. 2013). A most
recent study by Konotchick et al. (2013) conceptualized a depth-dependent physiology of seaweed by transcriptome analysis. The study with Ectocarpus aimed at
understanding the response to salinity showed the active function of γ-aminobutyric
acid (GABA) synthesized through a salt stress-induced putrescine degradation pathway (Dittami et al. 2011). Another study by the same group showed impregnation
of genomic alterations at metabolite level to stabilize the transition of evolutionary
colonization of alga from fresh water to marine habitat (Dittami et al. 2012). Sun
et al. (2015) developed a comparative transcriptome profile in Pyropia in response
to temperature stress indicating the complicated and diverse regulation mechanism,
such as upregulation of FAD in low-temperature stress and HSP in heat stress.
Similar results were obtained from the study on Fucus from the Arctic and subarctic
regions experiencing thermal stress (Smolina et al. 2016). These few comparative
studies thereby could define the ecophysiology of seaweeds but suffer from inevitable issue of tipping down the seaweed-specific regulatory elements in want of
assays precisely defining their roles by overexpression or knockdown approach.
As an example of breakthrough research on seaweed functional genomics, the
work published by Wang et al. (2015) and Oliveira et al. (2015) can be cited. The
former revealed the role of auxin polar transport, auxin signal transduction, crosstalk with other endogenous plant hormones and antioxidant systems, for adventitious buds formation in G. lichenoides explants in vitro. This work represented a
V. Gupta et al.
Though whole genome sequence studies explored some uncommon genomic
features related to primary and secondary metabolism in seaweeds, the large part of
the genomic information remained unannotated. Independent transcriptomics studies with de novo assembly and annotation of data define the regulations seaweed
possess for habiting the coastal environmental conditions. For example, the transcriptome for Ulva linza revealed the existence of land-specific genes, special photoprotective mechanism based on both LhcSR and PsbS, evidence of C4-like
carbon-concentrating mechanisms, multi-origin transporters for essential inorganic
nutrients, multiple and complex P450s for its colonization on coastal waters and
bloom formation (Zhang et al. 2012). A few more transcriptomic studies further
advance our knowledge towards the physiology and regulations in Sargassum (Liu
et al. 2014), Pyropia (Im et al. 2015) and Undaria (Shan et al. 2015). These studies
have revealed a few unknown pathways and highlighted the existence of specialized
mechanisms in seaweeds, which are quite distinct from terrestrial counterparts.
However, more than 40% of transcriptomic information generated from these studies remained unassigned as there is no BLAST hit for those regions. Thus unique
regulatory elements of seaweeds either at functional or physiological aspects could
not be defined. Missing such valuable information is a major setback towards understanding of seaweed unique physiology and functioning. Thus, integration of datasets from functional and comparative genomics is mandatory which can generate a
more accurate and holistic view of genes of unknown function (Xu et al. 2014). A
few studies have been carried out to understand the metabolic processes in response
to salinity and oxidative stress in a brown alga and were correlated with transcriptome data (Gravot et al. 2010; Dittami et al. 2011; Konotchick et al. 2013). A most
recent study by Konotchick et al. (2013) conceptualized a depth-dependent physiology of seaweed by transcriptome analysis. The study with Ectocarpus aimed at
understanding the response to salinity showed the active function of γ-aminobutyric
acid (GABA) synthesized through a salt stress-induced putrescine degradation pathway (Dittami et al. 2011). Another study by the same group showed impregnation
of genomic alterations at metabolite level to stabilize the transition of evolutionary
colonization of alga from fresh water to marine habitat (Dittami et al. 2012). Sun
et al. (2015) developed a comparative transcriptome profile in Pyropia in response
to temperature stress indicating the complicated and diverse regulation mechanism,
such as upregulation of FAD in low-temperature stress and HSP in heat stress.
Similar results were obtained from the study on Fucus from the Arctic and subarctic
regions experiencing thermal stress (Smolina et al. 2016). These few comparative
studies thereby could define the ecophysiology of seaweeds but suffer from inevitable issue of tipping down the seaweed-specific regulatory elements in want of
assays precisely defining their roles by overexpression or knockdown approach.
As an example of breakthrough research on seaweed functional genomics, the
work published by Wang et al. (2015) and Oliveira et al. (2015) can be cited. The
former revealed the role of auxin polar transport, auxin signal transduction, crosstalk with other endogenous plant hormones and antioxidant systems, for adventitious buds formation in G. lichenoides explants in vitro. This work represented a
V. Gupta et al.