268
in 2003, and the whole genome sequence was published in 2007 (Merchant et al.
2007). The genomic information has been coupled with mRNA expression analysis
of genes and is being used in the proteomic and metabolomic studies. The functional annotation of several genes in C. reinhardtii has led to elucidation of understanding of nitrate assimilation, photosynthesis, cell cycle regulation and various
other metabolic pathways (Jamers et al. 2009). At present, whole genome sequences
of various microalgae, viz. C. reinhardtii, C. vulgaris, Coccomyxa subellipsoidea,
Micromonas pusilla, Monoraphidium neglectum, Nannochloropsis gaditana,
Ostreococcus tauri, Ostreococcus luminarius, Phaeodactylum tricornutum,
Porphyridium purpureum, etc., are available (Hong and Lee 2015), which might
facilitate the scope of genetic improvement by transformation (Singh et al. 2016).
Early genomic investigation of C. reinhardtii carotenoid biosynthesis identified the
components of methylerythritol phosphate pathways and examined the light responsive nature of transcription of the carotenogenic machinery (Lohr et al. 2005).
Transcriptomics is the study of the functional importance of all genes that are
expressed. It provides information on the presence and relative abundance of RNA
transcripts and thus provides a better view of the active components in the cell than
a genomic approach (Jamers et al. 2009). Transcriptomics can be used either as an
actual identification tool or as a way to expand our fundamental knowledge and
understanding of certain metabolic pathways. Among the first algalomic studies, to
employ next-generation sequencing was a global transcriptomic examination of C.
reinhardtii during nitrogen starvation (Miller et al. 2010), which altered carbon flux
directly into fatty acid biosynthesis and downregulated genes involved in protein
biosynthesis and photosynthesis. Similar transcriptional analysis by Msanne et al.
(2012) reported immediate increase in the synthesis of starch, followed by TAG, in
C. reinhardtii and Coccomyxa sp. C-169 under nutrient depletion. Transcriptomic
analyses have identified 41 differentially regulated transcription factors in nitrogenstarved C. reinhardtii (Lv et al. 2013). With comparative transcriptome analysis in
a Neodesmus sp., a recent study (Chang et al. 2016) suggested involvement of triose
phosphate isomerase as a key enzyme regulating photosynthate partitioning between
fatty acid and starch biosynthesis in green microalgae. Using transcriptomics data
of C. reinhardtii, a microarray, i.e. a set of DNA sequences representing the entire
set of genes of an organism, arranged in a grid pattern for use in genetic testing, has
been developed, containing 10,000 oligonucleotide sequences, each presenting a
unique gene and covering nearly the full genome of the algae (htttp://www.chlamy.
org). Microarray analysis of C. reinhardtii exposed to copper revealed upregulation
of glutathione peroxidase and a probable glutathione S-transferase, which are
involved in oxidative stress defence mechanism (Jamers et al. 2006). Similarly,
microarray analysis of H. pluvialis under astaxanthin-inducing culture conditions
revealed decreased abundance of photosynthesis-related genes concurrent with
higher abundance of stress-related and signal transduction genes (Eom et al. 2006).
Modern next-generation sequencing technology has allowed the use of transcriptomic data to construct metabolic networks of Dunaliella tertiolecta (RismaniYazdi et al. 2011) and Botryococcus braunii (Molnár et al. 2012). Transcriptomics
have also been used to elucidate the transcriptional dynamics governing hydrogen
K. Chokshi et al.
in 2003, and the whole genome sequence was published in 2007 (Merchant et al.
2007). The genomic information has been coupled with mRNA expression analysis
of genes and is being used in the proteomic and metabolomic studies. The functional annotation of several genes in C. reinhardtii has led to elucidation of understanding of nitrate assimilation, photosynthesis, cell cycle regulation and various
other metabolic pathways (Jamers et al. 2009). At present, whole genome sequences
of various microalgae, viz. C. reinhardtii, C. vulgaris, Coccomyxa subellipsoidea,
Micromonas pusilla, Monoraphidium neglectum, Nannochloropsis gaditana,
Ostreococcus tauri, Ostreococcus luminarius, Phaeodactylum tricornutum,
Porphyridium purpureum, etc., are available (Hong and Lee 2015), which might
facilitate the scope of genetic improvement by transformation (Singh et al. 2016).
Early genomic investigation of C. reinhardtii carotenoid biosynthesis identified the
components of methylerythritol phosphate pathways and examined the light responsive nature of transcription of the carotenogenic machinery (Lohr et al. 2005).
Transcriptomics is the study of the functional importance of all genes that are
expressed. It provides information on the presence and relative abundance of RNA
transcripts and thus provides a better view of the active components in the cell than
a genomic approach (Jamers et al. 2009). Transcriptomics can be used either as an
actual identification tool or as a way to expand our fundamental knowledge and
understanding of certain metabolic pathways. Among the first algalomic studies, to
employ next-generation sequencing was a global transcriptomic examination of C.
reinhardtii during nitrogen starvation (Miller et al. 2010), which altered carbon flux
directly into fatty acid biosynthesis and downregulated genes involved in protein
biosynthesis and photosynthesis. Similar transcriptional analysis by Msanne et al.
(2012) reported immediate increase in the synthesis of starch, followed by TAG, in
C. reinhardtii and Coccomyxa sp. C-169 under nutrient depletion. Transcriptomic
analyses have identified 41 differentially regulated transcription factors in nitrogenstarved C. reinhardtii (Lv et al. 2013). With comparative transcriptome analysis in
a Neodesmus sp., a recent study (Chang et al. 2016) suggested involvement of triose
phosphate isomerase as a key enzyme regulating photosynthate partitioning between
fatty acid and starch biosynthesis in green microalgae. Using transcriptomics data
of C. reinhardtii, a microarray, i.e. a set of DNA sequences representing the entire
set of genes of an organism, arranged in a grid pattern for use in genetic testing, has
been developed, containing 10,000 oligonucleotide sequences, each presenting a
unique gene and covering nearly the full genome of the algae (htttp://www.chlamy.
org). Microarray analysis of C. reinhardtii exposed to copper revealed upregulation
of glutathione peroxidase and a probable glutathione S-transferase, which are
involved in oxidative stress defence mechanism (Jamers et al. 2006). Similarly,
microarray analysis of H. pluvialis under astaxanthin-inducing culture conditions
revealed decreased abundance of photosynthesis-related genes concurrent with
higher abundance of stress-related and signal transduction genes (Eom et al. 2006).
Modern next-generation sequencing technology has allowed the use of transcriptomic data to construct metabolic networks of Dunaliella tertiolecta (RismaniYazdi et al. 2011) and Botryococcus braunii (Molnár et al. 2012). Transcriptomics
have also been used to elucidate the transcriptional dynamics governing hydrogen
K. Chokshi et al.