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Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana.

Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC - Nat Commun (2012)

Bottom Line: The potential use of algae in biofuels applications is receiving significant attention.We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis.Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado 80401, USA.

ABSTRACT
The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.

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Genes conserved in photosynthetic stramenopiles.(a) Euler diagram showing the 363 genes that make up the StramenopilePhotoCut genes common to photosynthetic and absent in non-photosynthetic stramenopiles. Number of genes found in each sector is indicated. The centre yellow sector indicates genes unique for the photosynthetic Stramenopiles (not found in green or red lineages). (b) Chart showing the number of 'StramenopilePhotoCut' genes with select GO terms. 'StramenopilePhotoCut' genes with no GO terms are not indicated.
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f3: Genes conserved in photosynthetic stramenopiles.(a) Euler diagram showing the 363 genes that make up the StramenopilePhotoCut genes common to photosynthetic and absent in non-photosynthetic stramenopiles. Number of genes found in each sector is indicated. The centre yellow sector indicates genes unique for the photosynthetic Stramenopiles (not found in green or red lineages). (b) Chart showing the number of 'StramenopilePhotoCut' genes with select GO terms. 'StramenopilePhotoCut' genes with no GO terms are not indicated.

Mentions: Previous attempts have been made at establishing the minimal essential set of genes needed for photosynthesis, the 'GreenCut' of photosynthetic genes, which is a set of 597 orthologues that are conserved in plant and green algal lineages, but not in non-photosynthetic organisms1341. We decided to take advantage of the fact that there are both photosynthetic and non-photosynthetic stramenopiles to generate an analogous set of genes conserved in photosynthetic stramenopiles. To establish this 'StramenopilePhotoCut' of photosynthetic genes, orthologues common to N. gaditana and four photosynthetic stramenopiles (E. siliculosus, A. anophagefferens, T. pseudonana and P. tricornutum), but not present in non-photosynthetic stramenopiles (Phytophtora sojae, Phytophtora ramorum, Phytophtora infestans, Albugo laibachii or Blastocystis hominis), were selected, resulting in a list of 363 genes. (Fig. 3a and Supplementary Data 1). The majority of these genes have orthologues in the green and red algal lineages and 115 are found in the 'GreenCut2'41. However, 39 genes with homologues only found in photosynthetic stramenopiles are present in the genome (Supplementary Data 1). Similar to many genes found in the 'GreenCut', some of the 39 stramenopile-specific 'StramenopilePhotoCut' genes are of completely unknown function, but several of the genes have known domains, including several peptidases/proteases, DNA-binding proteins/transcription factors, and transport proteins, as well as genes that are thought to directly interact with the photosystems (Fig. 3b). Because of the high photoautotrophic growth rates exhibited by N. gaditana, we also characterized the complete pathways for synthesis of chlorophyll and accessory pigments (Supplementary Table S4). All expected genes could be identified except for those encoding the mevalonate (MVA) pathway for isopentenyl-pyrophosphate biosynthesis (see the analysis of bioenergy metabolic pathways).


Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana.

Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC - Nat Commun (2012)

Genes conserved in photosynthetic stramenopiles.(a) Euler diagram showing the 363 genes that make up the StramenopilePhotoCut genes common to photosynthetic and absent in non-photosynthetic stramenopiles. Number of genes found in each sector is indicated. The centre yellow sector indicates genes unique for the photosynthetic Stramenopiles (not found in green or red lineages). (b) Chart showing the number of 'StramenopilePhotoCut' genes with select GO terms. 'StramenopilePhotoCut' genes with no GO terms are not indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3293424&req=5

f3: Genes conserved in photosynthetic stramenopiles.(a) Euler diagram showing the 363 genes that make up the StramenopilePhotoCut genes common to photosynthetic and absent in non-photosynthetic stramenopiles. Number of genes found in each sector is indicated. The centre yellow sector indicates genes unique for the photosynthetic Stramenopiles (not found in green or red lineages). (b) Chart showing the number of 'StramenopilePhotoCut' genes with select GO terms. 'StramenopilePhotoCut' genes with no GO terms are not indicated.
Mentions: Previous attempts have been made at establishing the minimal essential set of genes needed for photosynthesis, the 'GreenCut' of photosynthetic genes, which is a set of 597 orthologues that are conserved in plant and green algal lineages, but not in non-photosynthetic organisms1341. We decided to take advantage of the fact that there are both photosynthetic and non-photosynthetic stramenopiles to generate an analogous set of genes conserved in photosynthetic stramenopiles. To establish this 'StramenopilePhotoCut' of photosynthetic genes, orthologues common to N. gaditana and four photosynthetic stramenopiles (E. siliculosus, A. anophagefferens, T. pseudonana and P. tricornutum), but not present in non-photosynthetic stramenopiles (Phytophtora sojae, Phytophtora ramorum, Phytophtora infestans, Albugo laibachii or Blastocystis hominis), were selected, resulting in a list of 363 genes. (Fig. 3a and Supplementary Data 1). The majority of these genes have orthologues in the green and red algal lineages and 115 are found in the 'GreenCut2'41. However, 39 genes with homologues only found in photosynthetic stramenopiles are present in the genome (Supplementary Data 1). Similar to many genes found in the 'GreenCut', some of the 39 stramenopile-specific 'StramenopilePhotoCut' genes are of completely unknown function, but several of the genes have known domains, including several peptidases/proteases, DNA-binding proteins/transcription factors, and transport proteins, as well as genes that are thought to directly interact with the photosystems (Fig. 3b). Because of the high photoautotrophic growth rates exhibited by N. gaditana, we also characterized the complete pathways for synthesis of chlorophyll and accessory pigments (Supplementary Table S4). All expected genes could be identified except for those encoding the mevalonate (MVA) pathway for isopentenyl-pyrophosphate biosynthesis (see the analysis of bioenergy metabolic pathways).

Bottom Line: The potential use of algae in biofuels applications is receiving significant attention.We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis.Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado 80401, USA.

ABSTRACT
The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.

Show MeSH
Related in: MedlinePlus