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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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Phylogenetic analysis of the N. gaditana genome.(a) Schematic phylogenetic tree of stramenopiles and photosynthetic algae. The tree is adapted from Eisenreich et al.,43 and Tyler et al.60 Filled green circles on the right indicate photosynthetic species. (b) The tree indicates the relationship between different strains of Nannochloropsis based on 18S ribosomal RNA gene sequences. (c) Venn diagram representation of shared/unique genes of N. gaditana in comparison with brown algae, diatoms, red algae and green algae. (d) N. gaditana gene models were compared with all previously sequenced genomes in the non-redundant protein database using BLASTp. The number of times an organism was the top BLASTp hits (E-value less than 1E-3) of a N. gaditana gene model is indicated.
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f2: Phylogenetic analysis of the N. gaditana genome.(a) Schematic phylogenetic tree of stramenopiles and photosynthetic algae. The tree is adapted from Eisenreich et al.,43 and Tyler et al.60 Filled green circles on the right indicate photosynthetic species. (b) The tree indicates the relationship between different strains of Nannochloropsis based on 18S ribosomal RNA gene sequences. (c) Venn diagram representation of shared/unique genes of N. gaditana in comparison with brown algae, diatoms, red algae and green algae. (d) N. gaditana gene models were compared with all previously sequenced genomes in the non-redundant protein database using BLASTp. The number of times an organism was the top BLASTp hits (E-value less than 1E-3) of a N. gaditana gene model is indicated.

Mentions: N. gaditana is a eustigmatophyte alga that is closely related to the Phaeophyceae (brown algae), with the most closely related organism having a fully sequenced genome being the multicellular brown alga, E. siliculosus (Fig. 2a)36. Among other species of Nannochloropsis, N. gaditana is most closely related to N. salina (Fig. 2b). To identify novel features of the N. gaditana genome, we determined which N. gaditana genes have homologues found in brown algae36 and the pelagophyte Aureococcus. anophagefferens37), green algae (Chlorella variabilis NC64A38 and C. reinhardtii13), red algae (Cyanidioschyzon merolae39), and diatoms (T. pseudonana40 and P. tricornutum14). This analysis confirms the close evolutionary proximity between the Eustigmatophyceae and Phaeophyceae (Fig. 2c), and provides us with 2,733 genes that are exclusive to N. gaditana, not found in the other algal genomes queried. This corresponds to 30.2% of the total gene repertoire in N. gaditana, which is similar to the fraction of unique genes found in T. pseudonana40, E. siliculosus36 and P. tricornutum14. Comparison of N. gaditana gene models to the non-redundant protein database (BLASTp) yielded top hits from a variety of organisms, the most frequent being stramenopiles (Fig. 2d), which was expected on the basis of the phylogeny of N. gaditana.


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)

Phylogenetic analysis of the N. gaditana genome.(a) Schematic phylogenetic tree of stramenopiles and photosynthetic algae. The tree is adapted from Eisenreich et al.,43 and Tyler et al.60 Filled green circles on the right indicate photosynthetic species. (b) The tree indicates the relationship between different strains of Nannochloropsis based on 18S ribosomal RNA gene sequences. (c) Venn diagram representation of shared/unique genes of N. gaditana in comparison with brown algae, diatoms, red algae and green algae. (d) N. gaditana gene models were compared with all previously sequenced genomes in the non-redundant protein database using BLASTp. The number of times an organism was the top BLASTp hits (E-value less than 1E-3) of a N. gaditana gene model is indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Phylogenetic analysis of the N. gaditana genome.(a) Schematic phylogenetic tree of stramenopiles and photosynthetic algae. The tree is adapted from Eisenreich et al.,43 and Tyler et al.60 Filled green circles on the right indicate photosynthetic species. (b) The tree indicates the relationship between different strains of Nannochloropsis based on 18S ribosomal RNA gene sequences. (c) Venn diagram representation of shared/unique genes of N. gaditana in comparison with brown algae, diatoms, red algae and green algae. (d) N. gaditana gene models were compared with all previously sequenced genomes in the non-redundant protein database using BLASTp. The number of times an organism was the top BLASTp hits (E-value less than 1E-3) of a N. gaditana gene model is indicated.
Mentions: N. gaditana is a eustigmatophyte alga that is closely related to the Phaeophyceae (brown algae), with the most closely related organism having a fully sequenced genome being the multicellular brown alga, E. siliculosus (Fig. 2a)36. Among other species of Nannochloropsis, N. gaditana is most closely related to N. salina (Fig. 2b). To identify novel features of the N. gaditana genome, we determined which N. gaditana genes have homologues found in brown algae36 and the pelagophyte Aureococcus. anophagefferens37), green algae (Chlorella variabilis NC64A38 and C. reinhardtii13), red algae (Cyanidioschyzon merolae39), and diatoms (T. pseudonana40 and P. tricornutum14). This analysis confirms the close evolutionary proximity between the Eustigmatophyceae and Phaeophyceae (Fig. 2c), and provides us with 2,733 genes that are exclusive to N. gaditana, not found in the other algal genomes queried. This corresponds to 30.2% of the total gene repertoire in N. gaditana, which is similar to the fraction of unique genes found in T. pseudonana40, E. siliculosus36 and P. tricornutum14. Comparison of N. gaditana gene models to the non-redundant protein database (BLASTp) yielded top hits from a variety of organisms, the most frequent being stramenopiles (Fig. 2d), which was expected on the basis of the phylogeny of N. gaditana.

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