Production Strain(s)

Aureococcus anophagefferens

Aureococcus anophagefferens is an algae that was first discovered in 1985. When in high bloom, it causes brown tide which severely affects the coastal ecosystem by damaging eelgrass beds and shellfish populations. Blooms occur seasonally along the eastern shore of USA. It generally grows in the shallow waters and can utilize organic and inorganic nutrients. Intense bloom occurs at places where the concentration of dissolved organic nitrogen and carbon levels is high.A. anophagefferens has an estimated genome size of about 32 Mb. DOE joint Genome Institute is planning to sequence its genome.

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Gobler CJ, et al. Proc Natl Acad Sci U S A 2011 Mar 15. [LINK]

Image source http://www.dec.ny.gov/outdoor/64824.html

  1. General
    Assembly Stats
    Number of contigs 5239
    N50 34096 bp
    Total assembly size 56.66 Mbp
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    Annotation v1 [GFF3]
    Coding region sequence v1 [FASTA]
    Protein sequence v1 [FASTA]

Auxenochlorella protothecoides

Auxenochlorella protothecoides(Trebouxiophyceae, Chlorophyta) is a genus of single-cell green algae, which was first described by Krger in 1894. It is highly regarded as one of the potential microalgae for biofuel production due to its ability to accumulate large quantity of lipids within the cell. A. protothecoides is 2-10 mm in diameter, coccoid and free-living. It contains multiple mitochondria, a single cup-shaped chloroplast, rigid cell wall and no flagella. Unlike most autotrophic green algae,A. protothecoides can not only live autotrophically by fixing sun?s energy through photosynthesis, but also can utilize organic components directly from environment for a heterotrophic growth. Compared with autotrophic cells, the intracellular structure and composition undergoes great changes in the heterotrophic cells. The most attractive phenomenon is the degradation of chloroplast and the accumulation of the oil bodies. The heterotrophic cells are more suitable for biodiesel production due to the increase in both biomass yield (51.2 g/L) and oil content (55.2%). Thus, A. protothecoides can serve as a model to study the mechanism of high oil accumulation and find ways to further reduce the cost of biodiesel.

Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes. Gao C, et al. BMC Genomics 2014 Jul 10. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=txid3075[orgn]

  1. General
    Assembly Stats
    Number of contigs 1386
    N50 35091 bp
    Total assembly size 22.9246 Mbp
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    Annotation v1 [GFF3]
    Coding region sequence v1 [FASTA]
    Protein sequence v1 [FASTA]

Bigelowiella natans

Bigelowiella natans is an amoeboflagellate algae that obtained its chloroplast by engulfing a photosynthetic eukaryote and retaining its chloroplast, a process called secondary endosymbiosis. The host cell also contains the nucleus, called nucleomorph, and the cytoplasm of the engulfed alga, though in reduced form. It belongs to family Chlorarachniophyceae. Members of this family are mixotrophic marine flagellates and amoeboflagellates with green plastids surrounded by four membranes.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Curtis BA, et al. Nature 2012 Dec 6. [LINK]

The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Rogers MB, et al. Mol Biol Evol 2007 Jan. [LINK]

Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Gilson PR, et al. Proc Natl Acad Sci U S A 2006 Jun 20. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Bigelowiella%20natans

  1. General
    Assembly Stats
    Number of contigs 3736
    N50 59463 bp
    Total assembly size 91.4059 Mbp
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    Annotation v1 [GFF3]

Chlamydomonas reinhardtii

Chlamydomonas is a genus of unicellular green algae found widely in fresh water, on damp soil, and a few occur in the sea. The cells are spherical or ellipsoidal. They have two equal flagella, present at the anterior end of the cell. The cell is surrounded by a fibrous glycoprotein cell wall. Chlamydomonas reinhardtii is the most commonly used laboratory species of Chlamydomonas since it can grow quickly with a generation time of 5 hrs and can form colonies on plates. In wild they survive in many different environments throughout the world. It is motile and cells of this species are haploid and can become diploid when deprived of nitrogen. Though photosynthetic, they can survive in total darkness in the presence of acetate. It has therefore been used as a model system to study photosynthesis and chloroplast biogenesis, mitochondrial biogenesis, flagellar assembly and motility, phototaxis, circadian rhythms, gametogenesis and mating, and cellular metabolism.C. reinhardtii has a genome size of about 120 Mb. It is haploid and has 17 chromosomes. It is an excellent system to study mutations as it has only a single copy of each gene.

  1. General
    Assembly Stats
    Scaffolds 1558
    Number of contigs 11385
    N50 44607bp
    Total assembly size 120.405 Mbp
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    Annotation v3 [GFF3]
    Coding region sequence v3 [FASTA]
    Protein sequence v3 [FASTA]

Chlamydomonas reinhardtii CC-503 cw92 mt+

Chlamydomonas is a genus of unicellular green algae found widely in fresh water, on damp soil, and a few occur in the sea. The cells are spherical or ellipsoidal. They have two equal flagella, present at the anterior end of the cell. The cell is surrounded by a fibrous glycoprotein cell wall. Chlamydomonas reinhardtii is the most commonly used laboratory species of Chlamydomonas since it can grow quickly with a generation time of 5 hrs and can form colonies on plates. In wild they survive in many different environments throughout the world. It is motile and cells of this species are haploid and can become diploid when deprived of nitrogen. Though photosynthetic, they can survive in total darkness in the presence of acetate. It has therefore been used as a model system to study photosynthesis and chloroplast biogenesis, mitochondrial biogenesis, flagellar assembly and motility, phototaxis, circadian rhythms, gametogenesis and mating, and cellular metabolism.C. reinhardtii has a genome size of about 120 Mb. It is haploid and has 17 chromosomes. It is an excellent system to study mutations as it has only a single copy of each gene.

Manganese deficiency in Chlamydomonas results in loss of photosystem II and MnSOD function, sensitivity to peroxides, and secondary phosphorus and iron deficiency. Allen MD, et al. Plant Physiol 2007 Jan. [LINK]

PIC1, an ancient permease in Arabidopsis chloroplasts, mediates iron transport. Duy D, et al. Plant Cell 2007 Mar. [LINK]

Integration of chloroplast nucleic acid metabolism into the phosphate deprivation response in Chlamydomonas reinhardtii. Yehudai-Resheff S, et al. Plant Cell 2007 Mar. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Chlamydomonas%20reinhardtii

  1. General
    Assembly Stats
    Scaffolds 1558
    Number of contigs 11385
    N50 44607bp
    Total assembly size 120.405 Mbp
  2. Experiments
    Expermients Link
    GMO vs WT Omics Pathway Viewer
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    DNA sequence [FASTA]
    Annotation [GFF3]
    Protein sequence [FASTA]
    Coding region sequence [FASTA]
    Gene sequence [FASTA]
    Transcriptomic analysis (HL_A4 vs UV4) [XSLS]
    Proteomic analysis (UVM4 A4 N1) Protein Summary [TEXT]

Chlorella sorokiniana str. 1228

Many microalgae in the genus Chlorella have been identified as viable production strains. Chlorella sp. 1228 is a clonal isolate derived from the Chlorella sorokiniana UTEX 1230 stock culture. Based on 18s rRNA identity, 1228 is most closely related to C. sorokiniana 1230 and Chlorella sp. 1412 (>99% similarity), yet the genomic content is distinct from these other Chlorella species, has unique phenotypic properties, and serves a reservoir of genomic material for genetic engineering applications.

  1. General
    Assembly Stats
    Number of contigs 64
    N50 2,415,094 bp
    Max contig size 4,567,720 bp
    Min contig size 15,864 bp
    Total assembly size 61,391,260 bp
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    DNA sequence v2 (IHQD) [FASTA]
    Annotation v2 [GFF3]
    Annotation Iprscan5 [TSV]
    Coding region sequence v2 [FASTA]
    Protein sequence v2 [FASTA]
    RNA-Seq Trinity [FASTA]

Chlorella sorokiniana UTEX 1230

Chlorella sorokiniana is one of the most productive strains identified for utilization as a biofuel feedstock (NAABB report). C. sorokiniana has an optimal growth temperature of 37°C, and is able to grow heterotropically on a variety of sugars that enhance oil accumulation. Growth in an optimized mixo- and heterotrophic bioreactor supplemented with glucose enabled C. sorokiniana UTEX 1230 to accumulate 30–40% of its cell mass as lipids (Rosenberg et al., 2014). Furthermore, while growing in the absence of nitrogen (following pre-growth with ammonia at dry weight production rates equivalent to growth in the presence of ammonia), the energy content of the algae increased by nearly 50% on a dry weight basis (Sangeeta Negi, personal communication).

  1. General
    Assembly Stats
    Number of contigs 20
    N50 4,091,730 bp
    Max contig size 5,120,617 bp
    Min contig size 57,538 bp
    Total assembly size 58,534,920 bp
  2. Download
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    DNA sequence v2 [FASTA]
    Annotation anticipated release date: 7/1/2015
    Coding region sequence anticipated release date: 7/1/2015
    Protein sequence anticipated release date: 7/1/2015
    RNA-Seq anticipated release date: 7/1/2015

Chlorella variabilis

Chlorella is a genus of about ten unicellular algal species that have small, spherical or ellipsoidal cells. They generally occur on soil and in freshwater. They have also been found as endosymbionts in invertebrate animals like Paramecium. They are non-flagellate cells but contain a vestigial flagellar apparatus. Reproduction is asexual and achieved by producing non motile autospores. They possess a firm polysaccharide cell wall which, in part, is made of sporopollenin like substance that occurs in the walls of the pollen grains of higher plants. It contains several essential nutrients and is a rich source of lutein, an important carotenoid. Chlorella species have been extensively studied and used in various practical applications in agriculture and biotechnology.

The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Blanc G, et al. Plant Cell 2010 Sep. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Chlorella%20variabilis

  1. General
    Assembly Stats
    Number of contigs 3810
    N50 27941bp
    Total assembly size 46.1595 Mbp
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    Protein sequence v1 [FASTA]

Chlorella vulgaris

Chlorella is a genus of about ten unicellular algal species that have small, spherical or ellipsoidal cells. They generally occur on soil and in freshwater. They have also been found as endosymbionts in invertebrate animals like Paramecium. They are non-flagellate cells but contain a vestigial flagellar apparatus. Reproduction is asexual and achieved by producing non motile autospores. They possess a firm polysaccharide cell wall which, in part, is made of sporopollenin like substance that occurs in the walls of the pollen grains of higher plants. It contains several essential nutrients and is a rich source of lutein, an important carotenoid. Chlorella species have been extensively studied and used in various practical applications in agriculture and biotechnology.

Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Wakasugi T, et al. Proc Natl Acad Sci U S A 1997 May 27. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Chlorella%20vulgaris

  1. General
    Assembly Stats
    Number of contigs 4754
    N50 20333 bp
    Total assembly size 37.3422 Mbp
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    Annotation v1 [GFF3]

Chondrus crispus

Chondrus crispus is a common marine seaweed found in both European and the Atlantic North American intertidal coastline. It appears like a low bushy plant which, when reproductive, may have small bumps near the tips. It appears in variety of forms and colours. The color varies from dark red to green and yellow or white depending on the sunlight and availability of nutrients. They are highly stress tolerant. Cell wall of C. crispus is rich in carrageenan, a mucopolysaccharide, which is used as thickener in food products

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Colln J, et al. Proc Natl Acad Sci U S A 2013 Mar 26. [LINK]

Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. Janoukovec J, et al. PLoS One 2013. [LINK]

Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae. Burger G, et al. Plant Cell 1999 Sep. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Chondrus%20crispus

  1. General
    Assembly Stats
    Number of contigs 3242
    N50 77748 bp
    Total assembly size 104.98 Mbp
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    DNA sequence v2 (IHQD) [FASTA]
    Annotation v2 [GFF3]
    Coding region sequence v2 [FASTA]
    Protein sequence v2 [FASTA]

Chrysochromulina tobin CCMP291

Chrysochromulina tobin is a small (4 micron) unicellular alga is naturally wall-less, being delineated solely by a plasma membrane. It lacks scales or additional extracellular structures. Chrysochromulina tobin is a haptophyte and lives in fresh to brackish water C tobin is also mixotrophic using a long haptonema to hunt bacterial prey.

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae). Blake T. Hovde , et al. Published: September 23, 2015. [LINK]

Image source http://www.washington.edu/news/2015/11/19/sequencing-algaes-genome-may-aid-biofuel-production/

  1. General
    Assembly Stats
    Number of contigs 3412
    N50 24114 bp
    Total assembly size 59.0731 Mbp
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    DNA sequence v1 [FASTA]
    Annotation v1 [GFF3]
    Protein sequence v1 [FASTA]

Coccomyxa subellipsoidea C-169

Coccomyxa is a genus of unicellular green alga. It comprises of number of species that are free living but also has species that form symbiotic relationships with lichens. Coccomyxa subellipsoidea C-169 is small, elongated, non-motile and well adapted to survive under extremely cold conditions of Antarctica.

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Blanc G, et al. Genome Biol 2012 May 25. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Coccomyxa%20subellipsoidea

  1. General
    Assembly Stats
    Number of contigs 29
    N50 1959569 bp
    Total assembly size 49.8266 Mbp
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    Annotation v2 [GFF3]
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    Protein sequence v2 [FASTA]

Cyanidioschyzon merolae

Cyanidioschyzon merolae is a primitive, unicellular red alga with a compact genome and a simple gene composition. It lives in sulphate-rich, acidic hot waters. The cell contains a single nucleus, a single mitochondrion and a single chloroplast. The genome size is about 16 Mbp, smallest of all photosynthetic eukaryotes. The majority of genes do not include introns and smaller copy numbers are found for typically high-copy number genes such as ribosomal genes. Because of the simple gene composition, C. merolae genome provides a model system for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.

A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae. Nozaki H, et al. BMC Biol 2007 Jul 10. [LINK]

Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Matsuzaki M, et al. Nature 2004 Apr 8. [LINK]

Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. Ohta N, et al. DNA Res 2003 Apr 30. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Cyanidioschyzon%20merolae

  1. General
    Assembly Stats
    Number of contigs 7
    Total assembly size 16.55 Mbp
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    Annotation v1 [GFF3]
    Coding region sequence v1 [FASTA]
    Protein sequence v1 [FASTA]

Cyanophora paradoxa

Cyanophora paradoxa is a freshwater species of Glaucophyte that is used as a model organism. C. paradoxa has two cyanelles or chloroplasts where nitrogen fixation occurs alongside the primary function of photosynthesis. The cyanelle genome of C. paradoxa strain LB 555 was sequenced and published in 1995. The nuclear genome was also sequenced and published in 2012.

Cyanophora BLAST and data download. [LINK]

Image source http://www.diark.org/diark/species_list/Cyanophora_paradoxa

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    Coding region sequence v1 [FASTA]
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Ectocarpus siliculosus

The brown algae are a group of almost exclusively marine photosynthetic organisms that are particularly abundant along rocky shorelines in temperate regions of the world. All the members of this group are multicellular. Ectocarpus siliculosus is a genomic model for filamentous brown algae.

  1. General
    Assembly Stats
    Number of contigs 13533
    N50 32613 bp
    Total assembly size 195.8 Mbp
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    Annotation v1 [GFF3]
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Emiliania huxleyi

The haptophyte Emiliania huxleyi is the dominant coccolithophoridforming mesoscale blooms across diverse regimes in the contemporaryoceans, often in regions inhospitable to other phytoplankton. Throughits ability to both calcify and photosynthetically fix carbon, thisgroup of small calcite-covered microalgae exerts profound control overglobal climate by mediating the exchange of CO2 between the atmosphereand the ocean and has done so for hundreds of thousands of years. Thisfirst sequenced haptophyte genome fills the gap in the eukaryotic treeof life. Genome sequence analysis will provide insights into key stepsin the biomineralization of calcite, light harvesting, acquiringnutrients and metabolism.E. huxleyi has a genome size of about 220 Mb

  1. General
    Assembly Stats
    Number of contigs 16921
    N50 29715 bp
    Max contig size x
    Min contig size x
    Total assembly size 167.68 Mbp
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    Annotation v1 [GFF3]
    Coding region sequence v1 [FASTA]
    Protein sequence v1 [FASTA]

Galdieria sulphuraria

Galdieria sulphuraria is a unicellular red alga found in hot sulphur springs. It is acido-thermophilic and can grow both autotrophically and heterotrophically in the dark. Other than living in extreme conditions of temperature and acidity, it can also tolerate high concentrations of metal ions. All these characteristics make it an ideal organism for genome sequencing and understanding the process of adaptation to extreme conditions and also genome evolution.The estimates for the genome size of Galdieria sulphuraria vary, depending on the method used, around 10 Mbp (Muravenko et al. 2001, Eur J Phycol 36: 227-232; Moreira et al., 1994, FEMS Microbiol Lett 122: 109-114) and 17 Mbp. There are also conflicting reviews on the chromosome number, ranging from 2 (microscopy: Muravenko et al. 2001, Eur J Phycol 36: 227-232) to 40 (pulsed-field eletrophoresis: Moreira et al., 1994, FEMS Microbiol Lett 122: 109-114)

Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Schnknecht G, et al. Science 2013 Mar 8. [LINK]

Image source http://www.ncbi.nlm.nih.gov/pubmed/23471408

  1. General
    Assembly Stats
    Number of contigs 518
    N50 116786 bp
    Total assembly size 13.712 Mbp
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    Annotation v1 [GFF3]
    Coding region sequence v1 [FASTA]
    Protein sequence v1 [FASTA]

Guillardia theta

Guillardia theta is a flagellate, unicellular alga that consists of a flagellate host cell, complete with mitochondria and nucleus, surrounding another cell with reduced cytoplasm that contains a plastid and a residual nucleus called nucleomorph. Formerly called Cryptomonas phi, plastid and nucleomorph containing cell has been acquired through secondary endosymbiosis by engulfing and retaining a red alga. Over time, it became a complex chloroplast losing most of its nuclear genes.G. theta nucleomorph consists of 3 chromosomes with a genome size of 551,264 base pairs. All the three chromosomes have been sequenced. Because of their reduced size and cell simplification, the nucleomorphs make an important model system to study genome and cell function and help in the understanding of the more complex chromosomes of typical nuclei.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Curtis BA, et al. Nature 2012 Dec 6. [LINK]

The highly reduced genome of an enslaved algal nucleus. Douglas S, et al. Nature 2001 Apr 26.[LINK]

Chloroplast protein and centrosomal genes, a tRNA intron, and odd telomeres in an unusually compact eukaryotic genome, the cryptomonad nucleomorph. Zauner S, et al. Proc Natl Acad Sci U S A 2000 Jan 4.[LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Guillardia%20theta

  1. General
    Assembly Stats
    Number of contigs 5126
    N50 40445 bp
    Total assembly size 87.1453 Mbp
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    Annotation v1 [GFF3]
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    Protein sequence v1 [FASTA]

Micromonas pusilla

Micromonas pusilla is a small eukaryotic alga measuring about 1 to 3 microns in length. It belongs to family Prasinophyceae which is believed to be the most primitive in the green lineage from which all other green algae and ancestors of land plants have descended. It includes several photosynthetic picoeukaryotic organisms. M. pusilla is pear shaped small alga. It contains one mitochondrion and one chloroplast and bears a single flagellum. It is found widely and exists as a complex of morphologically indistinguishable species that diverged long time ago (Slapeta et al). M. pusilla is identified as the most abundant picoeukaryotic organisms present in the oceanic and coastal regions. It therefore is a significant primary producer in the marine ecosystem. M. pusilla has a small genome of about 15 Mb. DOE Joint Genome Institute has sequenced the genome of two M. pusilla strains, NOUM17(RCC 299) and CCMP1545.

Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Worden AZ, et al. Science 2009 Apr 10. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/501

  1. General
    Assembly Stats
    Number of contigs 498
    N50 83658 bp
    Total assembly size 22 Mbp
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    Annotation v2 [GFF3]
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    Protein sequence v2 [FASTA]

Micromonas sp.

Isolates from a population of Micromonas which are clearly distinct from currently recognized species are tentatively designated at the species level. These unnamed isolates have not yet been characterized using traditional methods, or the species name has not yet been validly published.

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas. Science. 2009 April 10;324(5924):268-272 [LINK]

Image source http://genome.jgi.doe.gov/MicpuN3/MicpuN3.home.html

  1. General
    Assembly Stats
    Number of contigs 19
    N50 1,394,110 bp
    Max contig size x
    Min contig size x
    Total assembly size 21,109,300 Mbp
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    Annotation v2 [GFF3]
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    Protein sequence v2 [FASTA]

Monoraphidium neglectum

Microalga Monoraphidium neglectum is an oleaginous species with favourable growth characteristics and a high potential for crude oil production based on neutral lipid contents.

Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production. Bogen C, et al. BMC Genomics 2013 Dec 28. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Monoraphidium

  1. General
    Assembly Stats
    Number of contigs 12077
    N50 9150 bp
    Total assembly size 69.7118 Mbp
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    Annotation v1 [GFF3]
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Nannochloropsis gaditana

Nannochloropsis is a marine unicellular algae that is commonly cultivated in marine fish hatcheries as live feed for rotifers and fish larvae. Due to it's high content of omega-3-long-chain polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid and docosahexaenoic acid, it is a promising candidate for large scale production of these fatty acids.

Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. Corteggiani Carpinelli E, et al. Mol Plant 2014 Feb. [LINK]

Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana. Radakovits R, et al. Nat Commun 2012 Feb 21. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/11691

  1. General
    Assembly Stats
    Number of contigs 5619
    N50 21000 bp
    Total assembly size 221 Mbp
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Nannochloropsis oceanica

Unicellular marine algae have promise in providing sustainable and scalable feedstocks for the production of biofuels, although no single species has emerged as a preferred biofuel organism. Moreover, most marine algae lack adequate molecular and genetic resources, prerequisite for the rational engineering and synthetic biology of algal feedstocks. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high value lipid products. Genome sequences of the different species in this genus are becoming available and first success in applying reverse genetics make Nannochloropsis species attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Nannochloropsis is commonly cultivated in marine fish hatcheries as live feed for rotifers and fish larvae. Due to its high content of omega-3-long-chain polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid and docosahexaenoic acid, it is a promising candidate for large scale production of these fatty acids.

Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. Wei L, et al. BMC Genomics 2013 Aug 5. [LINK]

Image source

  1. General
    Assembly Stats
    Number of contigs 5851
    N50 12329 bp
    Total assembly size 27.6399 Mbp
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    Annotation v1 [GFF3]

Nannochloropsis salina CCMP1776

Nannochloropsis species were originally isolated and identified in marine environments, but are now also known to be present in fresh and brackish water. These Stramenopiles are small, 2-3μm nonmotile spheres. Individual species cannot be characterized by either light or electron microscopy, therefore species level differentiation is generally accomplished with rbcL chloroplast DNA and 18S rDNA sequence analysis. Nannochloropsis species differ from other related microalgae, such as diatoms and brown algae, in that they have chlorophyll a but lack chlorophyll b and c. In addition, they produce high concentrations of a range of pigments such as astaxanthin, zeaxanthin and canthaxanthin.

Nannochloropsis is considered a promising alga for industrial applications because of its ability to accumulate high levels of polyunsaturated fatty acids. It is also attractive as a production strain due to previous work showing high volume scalability of Nannochloropsis cultures. Moreover genetic manipulation is feasible in this organism and experiments aimed at the genetic improvement of Nannochloropsis are ongoing. Evidence exists that some strains are able to perform homologous recombination adding to the appeal of utilizing current generation genome engineering tools for Nannochloropsis manipulation. Currently, this organism is mainly used as an energy-rich food source for fish larvae and rotifers in aquaculture systems. Nevertheless, it has growing potential within the field of biofuel production.

Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. Corteggiani Carpinelli E, et al. Mol Plant 2014 Feb [LINK]

Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana . Radakovits R, et al. Nat Commun 2012 Feb 21 [LINK]

Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. Wei L, et al. BMC Genomics 2013 Aug 5 [LINK]

High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp. Kilian O el al. PNAS 2011 Dec 27 [LINK]

  1. General
    Assembly Stats
    Number of contigs 196
    N50 828,788 bp
    Max contig size 1,563,141 bp
    Min contig size 1165 bp
    Total assembly size 27,757,252 bp
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    Annotation v1 [GFF3]
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Nannochloropsis species CCMP1776

Nannochloropsis species were originally isolated and identified in marine environments, but are now also known to be present in fresh and brackish water. These Stramenopiles are small, 2-3μm nonmotile spheres. Individual species cannot be characterized by either light or electron microscopy, therefore species level differentiation is generally accomplished with rbcL chloroplast DNA and 18S rDNA sequence analysis. Nannochloropsis species differ from other related microalgae, such as diatoms and brown algae, in that they have chlorophyll a but lack chlorophyll b and c. In addition, they produce high concentrations of a range of pigments such as astaxanthin, zeaxanthin and canthaxanthin.

Nannochloropsis is considered a promising alga for industrial applications because of its ability to accumulate high levels of polyunsaturated fatty acids. It is also attractive as a production strain due to previous work showing high volume scalability of Nannochloropsis cultures. Moreover genetic manipulation is feasible in this organism and experiments aimed at the genetic improvement of Nannochloropsis are ongoing. Evidence exists that some strains are able to perform homologous recombination adding to the appeal of utilizing current generation genome engineering tools for Nannochloropsis manipulation. Currently, this organism is mainly used as an energy-rich food source for fish larvae and rotifers in aquaculture systems. Nevertheless, it has growing potential within the field of biofuel production.

Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. Corteggiani Carpinelli E, et al. Mol Plant 2014 Feb [LINK]

Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana . Radakovits R, et al. Nat Commun 2012 Feb 21 [LINK]

Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. Wei L, et al. BMC Genomics 2013 Aug 5 [LINK]

High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp. Kilian O el al. PNAS 2011 Dec 27 [LINK]

  1. General
    Assembly Stats
    Number of contigs 196
    N50 828,788 bp
    Max contig size 1,563,141 bp
    Min contig size 1165 bp
    Total assembly size 27,757,252 bp
  2. Download
    Download Link
    DNA sequence v1 [FASTA]
    Annotation v1 [GFF3]
    Protein sequence v1 [FASTA]

Ostreococcus tauri

Ostreococcus tauri is a small marine, photosynthetic organism measuring less than 1 mkm in size. It belongs to family Prasinophyceae which is believed to be the most primitive in the green lineage from which all other green algae, and ancestors of land plants have descended. It includes several photosynthetic picoeukaryotic organisms. O. tauri exhibits simple cellular structure with relatively large nucleus having one nuclear pore and a reduced cytoplasm with one chloroplast, one mitochondrion, and one Golgi body. It lacks flagella.O. tauri has a small genome of about 11.5 Mb with 14 or 18 chromosomes, which makes it an ideal organism for genome sequencing. Its genome has been sequenced at the Laboratoire Arago, Banyuls, France and is currently being annotated.

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. Blanc-Mathieu R, et al. BMC Genomics 2014 Dec 13. [LINK]

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Derelle E, et al. Proc Natl Acad Sci U S A 2006 Aug 1. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Ostreococcus%20tauri

  1. General
    Assembly Stats
    Number of contigs 1689
    N50 15097 bp
    Total assembly size 12.5723 Mbp
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    Annotation v2 [GFF3]
    Coding region sequence v2 [FASTA]
    Protein sequence v2 [FASTA]

Phaeodactylum tricornutum

Phaeodactylum tricornutum is a diatom belonging to the class Bacillariophyceae. Diatoms are unicellular algae that secrete intricate skeleton made of silica. Diatoms play an important role in marine ecosystem, particularly in the biogeochemical cycling of minerals like silica, and for global carbon fixation. They can be found in both fresh water and marine environments.P. tricornutum exists in three different morphological forms: oval, fusiform, and triradiate. Diatom researchers have established P. tricornutum as a model system to study diatom genomics. It is easy to culture and can be genetically transformed. It has a small genome size of about 30 Mb. The Joint Genome Institute is sequencing the genome of P. tricornutum.

Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Oudot-Le Secq MP, et al. Gene 2011 May 1. [LINK]

The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Bowler C, et al. Nature 2008 Nov 13. [LINK]

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Oudot-Le Secq MP, et al. Mol Genet Genomics 2007 Apr. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=Phaeodactylum%20tricornutum

  1. General
    Assembly Stats
    Number of contigs 179
    N50 417209 bp
    Total assembly size 27.4507 Mbp
  2. Download
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    Annotation v2 [GFF3]
    Coding region sequence v2 [FASTA]
    Protein sequence v2 [FASTA]

Picochlorum soleocismus DOE101

Picochlorum sp. strain DOE101 is a green microalgae within the phylum Chlorophyta and is most closely related to microalgae in the genus Nannochloris and Chlorella (Foflonker, 2015). This strain accumulates triacylglycerides (largely C16 and C18s) under nitrogen deplete conditions. This and other strains of Picochlorum are salt tolerant (Wang, 2014 ) and have the potential to be grown under a range of brackish cultivation conditions (von Alvensleben, 2013). Biomass production rates have been measure as high as 15.6 g/m2/day.

Foflonker, Fatima, Price, Dana C., Qiu, Huan, Palenik, Brian, Wang, Shuyi, Bhattacharya, Debashish. (2015) Genome of the halotolerant green alga Picochlorum sp. reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiol. 17(2) 1462-2920 [LINK]

Wang, S., Lambert, W., Giang, S., Goericke, R., and Palenik, B. (2014) Microalgal assemblages in a poikilohaline pond. J Phycol 50: 303–309

von Alvensleben N, Stookey K, Magnusson M, Heimann K (2013) Salinity Tolerance of Picochlorum atomus and the Use of Salinity for Contamination Control by the Freshwater Cyanobacterium Pseudanabaena limnetica. PLoS ONE 8(5): e63569

  1. Metadata
    Areal Productivity
    Biomass Accumulation (ePBR vs POND)
    Lipid Accumulation Profile
  2. General
    Assembly Stats
    Number of contigs 38
    N50 724,710 bp
    Max contig size 1,551,012 bp
    Min contig size 10,088 bp
    Total assembly size 15,252,578 bp
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    Annotation v1 [GFF3]
    Protein sequence v1 [FASTA]

Picochlorum sp.

Isolates from a population of Picochlorum which are clearly distinct from currently recognized species are tentatively designated at the species level. These unnamed isolates have not yet been characterized using traditional methods, or the species name has not yet been validly published.

Genome of the halotolerant green alga Picochlorum sp. reveals strategies for thriving under fluctuating environmental conditions. Foflonker F, et al. Environ Microbiol 2015 Feb. [LINK]

Image source http://onlinelibrary.wiley.com/doi/10.1002/btpr.686/pdf

  1. General
    Assembly Stats
    Number of contigs 883
    N50 126215 bp
    Total assembly size 13.39 Mbp
  2. Download
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    DNA sequence v1 (IHQD) [FASTA]
    Annotation v1 [GFF3]

Saccharina japonica

Saccharina genomes provide novel insight into kelp biology. Ye N, et al. Nat Commun 2015 Apr 24. [LINK]

Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): its structural features and phylogenetic analyses with other photosynthetic plastids. Wang X, et al. Mar Genomics 2013 Jun. [LINK]

Image source http://www.dec.ny.gov/outdoor/64824.html

  1. General
    Assembly Stats
    Number of contigs 35750
    N50 58867 bp
    Total assembly size 543.4 Mbp
  2. Download
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    Annotation v1 [GFF3]

Scenedesmus obliquus strain DOE0152Z

Scenedesmus obliquus strain DOE0152Z is a clonal isolate of DOE0152, a chlorophyte isolated in the Juergen Polle laboratory at Brooklyn College of CUNY under the NAABB consortium bioprospecting program. The original Scenedesmus obliquus strain DOE0152 was one of the top performing strains (indoor screening) with respect to biomass productivity and lipid content. Strain DOE0152 had also been tested outdoors at the TAMU Agrilife Pecos testbed site and is available from the UTEX culture collection (UTEX P9). Productivity data on the indoor and outdoor performance of strain DOE0152 can be found in the final NAABB report. [LINK]

  1. General
    Assembly Stats
    Number of contigs 2,812
    N50 152,111 bp
    Max contig size 2,334,183 bp
    Min contig size 2,277 bp
    Total assembly size 210,263,644 bp
  2. Download
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    DNA sequence v1 (IHQD) [FASTA]

Thalassiosira oceanica CCMP1005

The diatom Thalassiosira oceanica is an important oceanic primary producer that is adapted to chronic limitation of the essential nutrient iron.

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Lommer M, et al. Genome Biol 2012 Jul 26. [LINK]

Recent transfer of an iron-regulated gene from the plastid to the nuclear genome in an oceanic diatom adapted to chronic iron limitation. Lommer M, et al. BMC Genomics 2010 Dec 20. [LINK]

Image source http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=87606#

  1. General
    Assembly Stats
    Number of contigs 50892
    N50 3635 bp
    Total assembly size 92.1856 Mbp
  2. Download
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    Annotation v1 [GFF3]
    Protein sequence v1 [FASTA]

Thalassiosira pseudonana

Thalassiosira pseudonana is an unicellular algae, a diatom. Diatoms are found in almost all aquatic enviroments in the world. They have been well studied in both their natural habitat and in laboratory settings. Diatoms grow an outer silica shell, called a frustule, that is unique to each species. The silica shell can be preserved, and fossil frustules can be seen in sedimental layers as early as the Jurassic/Cretaceous period. Marine diatoms sequester large amounts of carbon, and are an important model organism for studies into the biology of oceanic carbon sequestration. Diatoms also furnish a significant portion of the world's oxygen supply. The removal of CO2 from surface water is also of interest. The genome sequence of a diatom will help elucidate a number of different biological and environmental questions, and provide a better understanding of diatom biology.

The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Bowler C, et al. Nature 2008 Nov 13. [LINK]

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Oudot-Le Secq MP, et al. Mol Genet Genomics 2007 Apr. [LINK]

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Armbrust EV, et al. Science 2004 Oct 1. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/54

  1. General
    Assembly Stats
    Number of contigs 115
    N50 1267198 bp
    Total assembly size 32.4374 Mbp
  2. Download
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    DNA sequence v2 (IHQD) [FASTA]
    Annotation v2 [GFF3]
    Coding region sequence v2 [FASTA]
    Protein sequence v2 [FASTA]

Volvox carteri

Volvox is a simple, spherical, multicellular green algae of order Volvocales. Volvocales are composed of two completely differentiated cell types, small somatic cells and few large, non motile reproductive cells. V. carteri is the commonly used lab species of Volvox. It has been extensively used for genetic analysis and evolutionary studies. Though it is haploid and asexual, it exhibits a sexual cycle that produces diploid zygotes which can withstand adverse conditions. It has an estimated genome size of about 120 Mb and Department of Energy's Joint Genome institute is in the process of sequencing it. Sequence analysis of Volvox offers unique opportunity to study the genetic basis for evolution of multicellular organisms.Volvox was first discovered by van Leeuwenhoek in 1700.

Evolution of an expanded sex-determining locus in Volvox. Ferris P, et al. Science 2010 Apr 16. [LINK]

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Prochnik SE, et al. Science 2010 Jul 9. [LINK]

Image source http://www.ncbi.nlm.nih.gov/genome/?term=volvox

  1. General
    Assembly Stats
    Number of contigs 11352
    N50 43981 bp
    Total assembly size 137.684 Mbp
  2. Download
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    DNA sequence v1 (IHQD) [FASTA]
    Annotation v1 [GFF3]
    Coding region sequence v1 [FASTA]
    Protein sequence v1 [FASTA]