5
multiple stressors arising from periodic tidal rhythms, for which there is no equivalent terrestrial counterpart (Kumar et al. 2011), are mostly at genetic levels. The
research on ecophysiology and economic trait mapping in seaweeds is underdetermined due to the lack of genetic markers. In order to illustrate this statement, a few
examples are the following : the 1940s witnessing the continued expansion in the
applications of in vitro techniques of plant cell and tissue culture and the same in
seaweed gaining momentum in the early 1990s (Reddy et al. 2008a,b, 2010) and
unavailability of genome editing technique in seaweed except a recent report of
Oertel et al. (2015) on developing suitable vectors and stable transformation in Ulva
mutabilis; however, this line of research gained gear in the 1990s in terrestrial plants
and now advanced to specific genome editing tools like TALEN and CRISPR/Cas9
(Kumar and Jain 2015). The attempts for genetic transformation in seaweeds and
associated challenges have been reviewed by Mikami (2013, 2014).
Nevertheless, scientific community made attempts to answer the seaweed high
diversity and adaptation to hypervariable environmental conditions through generation of expression sequence tag (EST) libraries and a few transcriptome profiles
(Collén et al. 2007; Dittami et al. 2009; Gravot et al. 2010; Pearson et al. 2010;
Dittami et al. 2011; Heinrich et al. 2012; Coelho et al. 2013). The genome level
understanding in seaweeds gained momentum after release of whole genome
sequence data of a brown alga Ectocarpus siliculosus (Dillwyn), Lyngbya (Cock
et al. 2010), a red alga Chondrus crispus (Irish moss) (Collen et al. 2013a, b) and
another brown alga Saccharina japonica (Ye et al. 2015). The whole genome
sequence revealed genomic features that evolved in these groups of organisms for
their successful propagation and proliferation in coastal environment. For example,
the Ectocarpus genome revealed the presence of a complex photosynthetic system
facilitating its propagation even in highly variable light conditions and flavonoid
pathway genes homologous to plants synthesizing high phenolic contents protecting the alga from ultraviolet radiations. An uncommon halide metabolism has been
deciphered based on the presence of 21 putative dehalogenases and 2 haloalkane
dehalogenases. Moreover, the genes and gene families associated with the development of multicellularity and evolution of the brown algal lineage have been identified (Cock et al. 2010). Similarly, the genome sequence of red alga has also
elucidated metabolic adaptations pertaining to halogen metabolism, synthesis of
oxylipins, microRNA and transcription factors for the development of multicellularity (Collen et al. 2013a, b). This study also revealed unique metabolic features
that are otherwise part of bacterial and fungal metabolism (cellulose synthesis and
cell wall remodelling) and are absent in genome of brown alga. The whole genome
analysis of S. japonica revealed gene families for iodine synthesis and concen tration
mechanism, biogenesis and remodelling of cell wall polysaccharides. The S. japonica is quite different from E. siliculosus in terms of more complex differentiation,
large blade size, higher polysaccharide content and high iodine accumulation. The
genome analysis could identify some of the striking features for these differences.
The phase-dependent Imm gene families were identified upregulated in gametophytic phase of S. japonica similar to E. siliculosus (Ye et al. 2015).
1 Macroalgal Functional Genomics: A Missing Area
multiple stressors arising from periodic tidal rhythms, for which there is no equivalent terrestrial counterpart (Kumar et al. 2011), are mostly at genetic levels. The
research on ecophysiology and economic trait mapping in seaweeds is underdetermined due to the lack of genetic markers. In order to illustrate this statement, a few
examples are the following : the 1940s witnessing the continued expansion in the
applications of in vitro techniques of plant cell and tissue culture and the same in
seaweed gaining momentum in the early 1990s (Reddy et al. 2008a,b, 2010) and
unavailability of genome editing technique in seaweed except a recent report of
Oertel et al. (2015) on developing suitable vectors and stable transformation in Ulva
mutabilis; however, this line of research gained gear in the 1990s in terrestrial plants
and now advanced to specific genome editing tools like TALEN and CRISPR/Cas9
(Kumar and Jain 2015). The attempts for genetic transformation in seaweeds and
associated challenges have been reviewed by Mikami (2013, 2014).
Nevertheless, scientific community made attempts to answer the seaweed high
diversity and adaptation to hypervariable environmental conditions through generation of expression sequence tag (EST) libraries and a few transcriptome profiles
(Collén et al. 2007; Dittami et al. 2009; Gravot et al. 2010; Pearson et al. 2010;
Dittami et al. 2011; Heinrich et al. 2012; Coelho et al. 2013). The genome level
understanding in seaweeds gained momentum after release of whole genome
sequence data of a brown alga Ectocarpus siliculosus (Dillwyn), Lyngbya (Cock
et al. 2010), a red alga Chondrus crispus (Irish moss) (Collen et al. 2013a, b) and
another brown alga Saccharina japonica (Ye et al. 2015). The whole genome
sequence revealed genomic features that evolved in these groups of organisms for
their successful propagation and proliferation in coastal environment. For example,
the Ectocarpus genome revealed the presence of a complex photosynthetic system
facilitating its propagation even in highly variable light conditions and flavonoid
pathway genes homologous to plants synthesizing high phenolic contents protecting the alga from ultraviolet radiations. An uncommon halide metabolism has been
deciphered based on the presence of 21 putative dehalogenases and 2 haloalkane
dehalogenases. Moreover, the genes and gene families associated with the development of multicellularity and evolution of the brown algal lineage have been identified (Cock et al. 2010). Similarly, the genome sequence of red alga has also
elucidated metabolic adaptations pertaining to halogen metabolism, synthesis of
oxylipins, microRNA and transcription factors for the development of multicellularity (Collen et al. 2013a, b). This study also revealed unique metabolic features
that are otherwise part of bacterial and fungal metabolism (cellulose synthesis and
cell wall remodelling) and are absent in genome of brown alga. The whole genome
analysis of S. japonica revealed gene families for iodine synthesis and concen tration
mechanism, biogenesis and remodelling of cell wall polysaccharides. The S. japonica is quite different from E. siliculosus in terms of more complex differentiation,
large blade size, higher polysaccharide content and high iodine accumulation. The
genome analysis could identify some of the striking features for these differences.
The phase-dependent Imm gene families were identified upregulated in gametophytic phase of S. japonica similar to E. siliculosus (Ye et al. 2015).
1 Macroalgal Functional Genomics: A Missing Area