Organisms

What are Stramenopiles?

Stramenopiles are a "crown" taxon that evolved about 300 million years ago and radiated after the Cretaceous Period. They include both photosynthetic and nonphotosynthetic taxa. Photosynthetic members include brown seaweeds, diatoms, chrysophytes and several other groups varying in morphology from simple unicells to more highly complex structures. These autotrophic eukaryotes impact many of the earth's biogeochemical cycles (e.g. sulfur and nitrogen loading) and serve as primary producers that fix a significant portion of the total CO2 processed on earth. The stramenopiles represent a major eukaryotic group that is taxonomically distinct from the chlorophytic or rhodophytic lineages of autotrophs.

hetersigma bullet

Why Chloroplast Genomes?

Chloroplasts are intracellular organelles. They carry their own genome that encodes for many (but not all) of the genes essential for photosynthesis. With respect to chloroplast genomic studies, almost exclusive emphasis has been placed on the generation of data from the chlorophytic lineage of autotrophs. About 15 chlorophytic chloroplast genomes have been sequenced in their entirety and there are many more projects ongoing, particularly land plants. However, to date, only minimal data exists with respect to chloroplast genome sequences for non-chlorophyll b-containing algae (of the approximately 100,000 known species) despite their important contributions to ecosystem function.

hetersigma bullet

 

NSF logo

This project is a joint effort between the research groups of Dr. Rose Ann Cattolico and Dr. Gabrielle Rocap at the University of Washington. Some of this work is part of a larger Assembling the Tree of Life Project-- Deep Brown.

This material is based upon work supported by the National Science Foundation under Grants No. 0523756 and 0629554. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF)

hetersigma bullet

References

The mesozoic radiation of eukaryotic algae: The portable plastid hypothesis
Grzebyk D, Schofield O, Vetriani C, Falkowski PG
JOURNAL OF PHYCOLOGY
39 (2): 259-267 APR 2003

Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns
De las Rivas J, Lozano JJ, Ortiz AR
GENOME RESEARCH
12 (4): 567-583 APR 2002

Primary and secondary endosymbiosis and the origin of plastids
McFadden GI
JOURNAL OF PHYCOLOGY
37 (6): 951-959 DEC 2001

Phylogenetic relationships of the 'golden algae' (haptophytes, heterokont chromophytes) and their chloroplasts
Medlin, L. K., W. H. C. F. Kooistra, D. Potter, G. W. Saunders and R. A. Andersen
PLANT SYSTEMATICS AND EVOLUTION
11: 187-219 1997

Apedinella radians

Name
Apedinella radians
Class
Dictyochophyceae, NCBI Taxonomy
Size

Length: 6 - 8 µm

Width: 8 - 10 µm

Morphology
Unicellular
Toxic
No
Regime
North Atlantic Europe
Strain Source
CCMP1767

Fosmid Ends

Apedinella radians Fosmid Ends

 

fosmid Plate
Raw End Sequences Best Blast Results
apra1f1_fp01
Fasta (3/31/2008)
Excel
apra1f1_fp02 Fasta (4/10/08) Excel


Sequences & Annotations

Asterosiphon dichotomus

Name
Asterosiphon dichotomus
Class
Xanthophyceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Strain Source
UTEX, LB 2066

Fosmid Ends

fosmid Plate
Raw End Sequences Best Blast Results
asdi1f2_fp01
Fasta (8/4/08)
Excel
asdi1f2_fp02 Fasta (8/7/08)
Excel


Aurearena cruciata

Name
Aurearena cruciata
Class
Aurearenophyceae, NCBI Taxonomy
Size
Morphology
Unicellular
Toxic
No
Regime
Marine coastal
Strain Source NIES-1865

Aureoumbra lagunensis

Name Aureoumbra lagunensis
Class Pelagophyceae, NCBI Taxonomy
Size

Length: 4 - 6 µm

Width: 4 - 6 µm

Morphology Unicellular, coccoid
Toxic
Yes
Regime Open and coastal oceans
Strain Source CCMP1507




Aureoumbra lagunensis belongs to the class Pelagophyceae, a class with 11 genera, many monotypic, comprised only of marine species. They are very common and abundant in the open oceans and can form harmful blooms in coastal regions. Aureoumbra is a small, non-flagelated unicell. The organism forms persistent, dense brown tides in Texas embayments and lagoons. High cell densities cause severe reduction in light penetration and compromise the health of pelagic and benthic ecosystems.

Fosmid Ends

Aureoumbra lagunensis Fosmid Ends

 

fosmid Plate
Raw End Sequences Full Blast Results
(big files)
Best Blast Results
aur1f1_fp01
Fasta (8/14/06)
RawBlast.zip
Excel
aur1f1_fp02
Fasta (8/14/06)
  Excel


Bolidomonas pacifica

Name Bolidomonas pacifica
Class Bolidophyceae, NCBI Taxonomy
Size 2-3 µm
Morphology Unicellular, flagellate
Toxic No
Regime Equatorial Pacific Ocean
Strain Source CCMP1866



Fosmid Ends

Bolidomonas pacifica Fosmid Ends

 

Fosmid Plate
Raw End Sequences Best Blast Results
bol1f1_fp01
Fasta (5/2/07)
Excel
bol1f1_fp02
Fasta (5/9/07)
Excel
bol1f1_fp03
Fasta (5/24/07)
Excel
bol1f1_fp02x2 Fasta (6/22/07) Excel
bolf1_fp04
Fasta (7/10/07)
Excel
bolf1_fp05 Fasta (8/11/07) Excel
bolf2_fp01 Fasta (1/14/08)
Excel
bolf2_fp02 Fasta (1/14/08) Excel
bolf2_fp03 Fasta (3/18/2008)
Excel
bolf2_fp04 Fasta (3/18/2008) Excel
bol1f3_fp01 Fasta (5/19/2008) Excel
bol1f3_fp02 Fasta (5/19/2008) Excel
bol1f3_fp03 Fasta (6/26/2008) Excel
bol1f3_fp04 Fasta (6/26/2008)
Excel
bol1f3_fp01x2 Fasta (7/29/2008) Excel
bol1f3_fp02x2 Fasta (7/29/2008) Excel
bol1f3_fp05 Fasta (7/29/2008) Excel
bol1f1_summary Excel (4/1/2009)
bol1f3_summary Excel (4/1/2009)
bol1f3_summary Excel (4/1/2009)

 


Botrydium cystosum

Courtesy of UTEX

Name
Botrydium cystosum
Class
Xanthophyceae, NCBI Taxonomy
Size
Morphology
Unicellular
Toxic
Regime
Strain Source UTEX 157

Fosmid Ends

Botrydium cystosum Fosmid Ends

fosmid plate Raw sequence Best Blast Results
bot1f1_fp01 Fasta Excel (8/23/07)
bot1f1_fp02
Fasta
Excel (9/21/07)
bot1f1_fp03 Fasta
Excel (3/11/08)
bot1f1_fp04 Fasta
Excel (3/11/08)
bot1f1_fp05 Fasta and Fasta and Fasta2 Excel and Excel (3/25/10) and Excel2 (8/26/10)
bot1f1_fp06_q1q2 Fasta Excel (10/10)
bot1f1_fp06_q3q4 Fasta Excel (10/10)
bot1fi_summary   Excel (6/2010)

Chattonella subsalsa

Chatt pic
Name Chattonella subsalsa
Class Raphidophyceae, NCBI Taxonomy
Size

Length: 25 - 50 µm

Width: 15 - 21 µm

Morphology Unicellular
Toxic
Yes
Regime Brackish waters, estuaries, canals and ponds
Strain Source CCMP217



Chattonella subsalsa
belongs to the class Raphidophyceae. This class comprises about six genera (half freshwater, half marine). Selected marine genera have been extensively studied because of their toxicity (Horner et al. 1997, Marshall et al. 2003). The relationships of the Pinguiophyceae and Raphidophyceae are largely unresolved.

Chattonella subsalsa
represents a genus that has caused immense losses to the finfish aquaculture industry worldwide [e.g.157 million dollars worth of farmed yellowtail in Japan (Okaichi 1989)]. Brevetoxin-like compounds are produced by this alga (Khan et al. 1995)




References:



Horner, R. A., D. L. Garrison and F. G. Plumley (1997). Harmful algal blooms and red tide problems on the US west coast. Limnol. Ocean. 42: 1076-1088


Khan, S., M. S. Ahmed, O. Arakawa and Y. Onoue (1995). Properties of neurotoxins separated from a harmful red tide organism Chattonella marina. The Israeli Journal of Aquaculture-Bamidgeh 47: 137-141


Marshall, J.-A., P. D. Nichols, B. Hamilton, R. J. Lewis and G. M. Hallegraeff (2003). Ichthyotoxicity of Chattonella marina (Raphidophyceae) to damselfish (Acanthochromis polycanthus): the synergistic role of reactive oxygen species and free fatty acids. Harmful Algae 2: 273-281


Okaichi, T. (1989). Red tide problems in the Seto Inland Sea, Japan. in Red Tides: Biology, Environmental Science and Toxicology. T. Okaichi, D. Anderson and T. Nemoto, eds. Elsevier, New York. pp. 137-142

Fosmid Ends

Chattonella subsalsa Fosmid Ends

 

Fosmid Plate
Raw End Sequences Best Blast Results
chat1f1_fp01
Fasta
Excel
chat1f1_fp02xy1 Fasta
Excel
chat1f1_fp02xy2 Fasta Excel
chat1f1_fp03xy1 Fasta
Excel
chat1f1_fp04xy1
Fasta
Excel
chat1f2_fp02 Fasta
Excel
chat1f2_fp01 Fasta Excel
chat1_f3_fp01 Fasta (1/14/08)
Excel
chat1_f3_fp02
Fasta (1/14/08) Excel
chat1f3_fp03 Fasta (3/31/08) Excel
chat1f3_fp04 Fasta (3/27/08)
Excel
chat1f1_summary Excel (4/1/2009)
chat1f2_summary Excel (4/1/2009)
chat1f3_summary Excel (4/1/2009)

 

Chlorobotrys regularis

Name Chlorobotrys regularis
Class Eustigmatophyceae
Size
Morphology
Toxic

Regime Freshwater; Yorkshire, England
Strain Source CCAP810/1


Chloromorum toxicum

Name Chloromorum toxicum
Class Unclassified Stramenopile, NCBI Taxonomy
Size
Morphology Flagellate
Toxic
Yes
Regime Coastal regions
Strain Source




















REFERENCES:

GROWTH, NUTRIENT UTILIZATION AND EVIDENCE FOR TOXIN PRODUCTION BY THE NEW TOXIC FLAGELLATE CHLOROMORUM TOXICUM

Carmelo R. Tomas, Andrea Bourdelais, Lucille E. Tomas and Avery O. Tatters
Center for Marine Science, University of North Carolina at Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409
3rd Symposium on Harmful Algae in the U.S.
October 2005

Fosmid Ends

Chloromorum toxicum Fosmid Ends


Fosmid Plate
Raw End Sequences Full Blast Results
(big files)
Best Blast Results
chlo1_fp01x1
Fasta
  Excel
chlo1_fp01y1
Fasta
   
chlo1f1_fpo2 Fasta   Excel

Choristocarpus tenellus

Name
Choristocarpus tenellus
Class
Choristocarpaceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Strain Source KU-1152

Fosmid Ends


Fosmid Plate
Raw End Sequences Best Blast Results
cho1f1_fp01x1
Fasta Excel
cho1f1_fp02 Fasta
Excel
cho1f1_fp03
Fasta
Excel
cho1f1_fp04 Fasta (10/4/08)
Excel

Chrysowaernella hieroglyphica

Name
Chrysowaernella hieroglyphica
Class
Size
Morphology
Toxic
Regime
Strain Source

Fosmid Ends

Fosmid Plate
Raw End Sequences Best Blast Results
chhi1f1_fp01 Fasta (2/19/08) Excel
chhi1f1_fp02 Fasta (2/19/08)
Excel
chhi1f1_fp03
Fasta (12/1/08)
Excel
chhi1f1_fp04 Fasta (12/3/08) Excel

 


Desmarestia aculeata

Courtesy of KU-MACC

Name
Desmarestia aculeata
Class
Phaeophyceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Strain Source KU-1141

Desmarestia phaeophyceae

Name
Desmarestia phaeophyceae
Class
Size
Morphology
Toxic
Regime
Strain Source

Fosmid Ends

Fosmid Plate
Raw End Sequences Best Blast Results
des1f1_fp01 Fasta (2/19/08) Excel
des1f1_fp02 Fasta (2/19/08)
Excel
des1f1_fp04 Fasta (2/20/09) Excel
des1f1_fp06 Fasta (2/20/09) Excel

 


Dictyocha speculum

Courtesy of CCMP

Name
Dictyocha speculum
Class
Dictyochophyceae, NCBI Taxonomy
Size

Length: 16 - 72 µm

Width: 16 - 56 µm

Morphology
Unicellular
Toxic
No
Regime
North Atlantic, Baltic Sea
Strain Source CCMP1381

Fosmid Ends

Fosmid Plate
Raw End Sequences Best Blast Results
disp1f2_fp01 Fasta (8/18/08) Excel
disp1f2_fp02 Fasta (8/18/08)
Excel

 


Dictyota dichotoma

Courtesy of KU-MACC

Name Dictyota dichotoma
Class Phaeophyceae, NCBI Taxonomy
Size 5-20 cm
Morphology Branched, symmetrical
Toxic
No
Regime Warm, coastal waters
Strain Source

KU-1070




Fosmid Ends

Dictyota dichotoma Fosmid Ends

 

fosmid Plate
Raw End Sequences Best Blast Results
dicty1f1_fp01
Fasta (5/12/2008)
Excel
dicty1f1_fp02 Fasta (5/12/08) Excel


Eustigmatos magna

Courtesy of CCMP

Name
Eustigmatos magna
Class
Eustigmatophyceae, NCBI Taxonomy
Size

Length: 4 - 12 µm

Width: 4 - 12 µm

Morphology
Unicellular
Toxic
No
Regime
Freshwater
Strain Source CCMP387

Halopteris filicina

Name
Halopteris filicina
Class
Phaeophyceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Strain Source KU-690

Heterococcus caespitosus

Name
Heterococcus caespitosus
Class
Xanthophyceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Strain Source
UTEX 385

Fosmid Ends

fosmid Plate
Raw End Sequences Best Blast Results
het1f1_fp02
Fasta (7/28/08)
Excel
het1f1_fp03 Fasta (8/1/08)
Excel


Heterosigma akashiwo CCMP452

Heterosigma akashiwo strain 452
Name Heterosigma akashiwo
Class Raphidophyceae, NCBI Taxonomy
Size

Length: 10 - 15 µm

Width: 10 - 14 µm

Morphology Unicellular
Toxic
Yes
Regime Coastal regions world-wide
Strain Source
CCMP452



hetersigma bullet

About Heterosigma akashiwo
Heterosigma akashiwo (formerly Olisthodiscus luteus) is a naturally wall-less, toxic alga that blooms in coastal regions world-wide. In the field, Heterosigma forms massive brown tides that impact the survival of eco-cohorts at every trophic level. This alga has been shown to kill finfish, compromise fish and sea urchin egg development and impact copepod as well as oyster survival. Heterosigma blooms have caused economic losses amounting to many millions of dollars in fish species, including salmonids, sea bream, yellowtail, sea bass and flounder and commercially important invertebrates such as oysters and clams. It has been suggested that Heterosigma produces a species-specific allelopathic substance that can affect the survival of algae and possibly other phytoplankton. Heterosigma's ability to flourish in these diverse habitats is probably due in part to: (a) its tolerance of a wide range of environmental conditions (e.g., a salinity range of 2 to >50; temperature range of <5°C to >30°C) and adaptability to anthropogenic growth conditions; and (b) the ability of Heterosigma resting cells to survive long-range transport by natural currents and ship ballast water.

hetersigma bullet
About the Chloroplast Genome
The 154 Kb chloroplast genome of Heterosigma akashiwo strain 452 contains an inverted repeat sequence of 22kb separating two single-copy regions of 37 and 73 kb, respectively. Genes not normally found in terrestrial plants or green algal chloroplast genomes are present in Heterosigma plastid DNA (e.g. the small subunit of Rubisco; a prokaryotic-like two-component signal transduction array). Genes are tightly packed (often overlapping) lack introns and do not have the multiple promoter domains frequently associated with the chloroplasts genes of green algae and terrestrial plants.

hetersigma bullet


References:

A conserved His-Asp signal response regulator-like gene in Heterosigma akashiwo chloroplasts
Jacobs,M.A., Connell,L. and Cattolico,R.A.
PLANT MOLECULAR BIOLOGY
41 (5), 645-655 (1999)

Chloroplast DNA: Structure and organization of chromophyte and rhodophyte plastid genomes: Implications for the ancestry of plastids
Shivji, M. S., N. Li and R. A. Cattolico
MOLECULAR AND GENERAL GENETICS
232: 65-73 1992

Synchronous growth and plastid replication in the naturally wall-less alga Olisthodiscus luteus
Cattolico, R. A., J. C. Boothroyd and S. P. Gibbs
PLANT PHYSIOLOGY
57: 497-503. 1976

Fosmid Ends

Heterosigma akashiwo: Strain 452


Fosmid End Sequences


These files combine read data from all plates of 452 fosmids into two files.

Fosmid Plate
Raw End Sequences Full Blast Results
(big files)
Blast Best Results
Hak452_x Hak452_x.fasta.zip
Hak452_x.blast.zip Hak452_x.best.xls
Hak452_y Hak452_y.fasta.zip Hak452_y.blast.zip Hak452_y.best.xls



 


Heterosigma akashiwo NIES293

Name Heterosigma akashiwo
Class Raphidophyceae, NCBI Taxonomy
Size 10-15 µm
Morphology Unicellular
Toxic
Yes
Regime Coastal regions world-wide
Strain Source
NIES-293



hetersigma bullet

About Heterosigma akashiwo
Heterosigma akashiwo (formerly Olisthodiscus luteus) is a naturally wall-less, toxic alga that blooms in coastal regions world-wide. In the field, Heterosigma forms massive brown tides that impact the survival of eco-cohorts at every trophic level. This alga has been shown to kill finfish, compromise fish and sea urchin egg development and impact copepod as well as oyster survival. Heterosigma blooms have caused economic losses amounting to many millions of dollars in fish species, including salmonids, sea bream, yellowtail, sea bass and flounder and commercially important invertebrates such as oysters and clams. It has been suggested that Heterosigma produces a species-specific allelopathic substance that can affect the survival of algae and possibly other phytoplankton. Heterosigma's ability to flourish in these diverse habitats is probably due in part to: (a) its tolerance of a wide range of environmental conditions (e.g., a salinity range of 2 to >50; temperature range of <5°C to >30°C) and adaptability to anthropogenic growth conditions; and (b) the ability of Heterosigma resting cells to survive long-range transport by natural currents and ship ballast water.

hetersigma bullet
About the Chloroplast Genome
The 154 Kb chloroplast genome of Heterosigma akashiwo strain 452 contains an inverted repeat sequence of 22kb separating two single-copy regions of 37 and 73 kb, respectively. Genes not normally found in terrestrial plants or green algal chloroplast genomes are present in Heterosigma plastid DNA (e.g. the small subunit of Rubisco; a prokaryotic-like two-component signal transduction array). Genes are tightly packed (often overlapping) lack introns and do not have the multiple promoter domains frequently associated with the chloroplasts genes of green algae and terrestrial plants.

hetersigma bullet


References:

A conserved His-Asp signal response regulator-like gene in Heterosigma akashiwo chloroplasts
Jacobs,M.A., Connell,L. and Cattolico,R.A.
PLANT MOLECULAR BIOLOGY
41 (5), 645-655 (1999)

Chloroplast DNA: Structure and organization of chromophyte and rhodophyte plastid genomes: Implications for the ancestry of plastids
Shivji, M. S., N. Li and R. A. Cattolico
MOLECULAR AND GENERAL GENETICS
232: 65-73 1992

Synchronous growth and plastid replication in the naturally wall-less alga Olisthodiscus luteus
Cattolico, R. A., J. C. Boothroyd and S. P. Gibbs
PLANT PHYSIOLOGY
57: 497-503. 1976

Fosmid Ends

Heterosigma akashiwo: Strain 293


Fosmid End Sequences


Fosmid Plate
Raw End Sequences
Full Blast Results
(big files)
Blast Best Results
Hak293_x Hak293_x.fasta.zip
Hak293_x.blast.zip Hak293_x.best.xls
Hak293_y Hak293_y.fasta.zip Hak293_y.blast.zip Hak293_y.best.xls
f2_fp02x1q3q4 f2_fp02x1q3q4.fasta.zip f2_fp02x1q3q4.blast.zip f2_fp02x1q3q4.best.xls
f2_fp02y1q3q4 f2_fp02y1q3q4.fasta.zip f2_fp02y1q3q4.blast.zip f2_fp02y1q3q4.best.xls
haka293f2_fp03x1 fp03x1.fasta.zip
fp03x1.RawBlast.zip fp03x1.best.xls
haka293f2_fp03y1 fp03y1.fasta.zip fp03y1.RawBlast.zip fp03x1.best.xls



Mallomonas splendens

Courtesy of CCMP

Name
Mallomonas splendens
Class
Synurophyceae, NCBI Taxonomy
Size

Length: 40 - 60 µm

Width: 10 - 16 µm

Morphology
Unicellular
Toxic
No
Regime
Freshwater
Strain Source CCMP1782

Fosmid Ends

Fosmid plate Raw sequence Best Blast Results
masp1_fp01 Fasta Excel (3/31/08)
masp2_fp02 Fasta
Excel (3/11/08)

Nannochloropsis oculata

Nann pic
Name Nannochloropsis oculata
Class Eustigmatophyceae, NCBI Taxonomy
Size

Length: 1-2 µm

Width: 1-2 µm

Morphology Unicellular, sphere
Toxic
No
Regime ???
Strain Source CCMP525



Nannochloropsis oculata
belongs to the class Eustigmatophyceae. This class consists of about six genera that were separated from the Xanthophyceae; it seems likely that more genera will be transferred into the class from the Xanthophyceae in the future. The eustigmatophytes are small microalgae that are planktonic or grow attached to various substrates. They are unique in lacking chlorophyll pigments other than chl a (Fisher et al. 1998).

Nannochloropsis oculata
is one of the five identified species of the genus. These species are characterized by small cells with a simple morphology and typically live in salt-water habitats. Nannochloropsis species are widely used as food in aquaculture and have been proposed as a commercial source for the dietary supplement a omega-3 fatty acid (Sukenik et al. 1989).

 

 


References:

Fisher, T., T. Berner, D. Iluz and Z. Dubinsky (1998).
The kinetics of photoacclimation response of Nannochloropsis sp (Eustigmatophyceae): A study of changes in ultrastructure and PSU density. J. Phycol. 34: 818-824.

Sukenik, A., Y. Carmeli and T. Berner (1989). Regulation of fatty acid composition by irradiance level in the eustigmatophyte Nannochloropsis sp. J. Phycol. 25: 686-692.

Fosmid Ends

Nannochloropsis oculata

 

Fosmid End Sequences


 

Fosmid Plate
Raw End Sequences  Best Blast Results
fp01 and fp02
fasta
best.xls
f1_fp04
fasta
best.xls
fp03
fasta
best.xls
fp05
fasta

best.xls (05/23/07)

re-posted (05/24/07)

fp06 (8/11/07)
fasta best.xls
nan1f2_fp01 fasta (5/9/2008)
best.xls
nan1f2_fp02 fasta (5/9/2008)
best.xls
nan1f2_fp03 fasta best.xls
nan1f2_fp04 fasta best.xls
nan1f2_fp05 fasta best.xls
nan1f3_fp01 fasta (11/19/2008) excel
nan1f3_fp01x2 fasta (11/19/2008) excel
nan1f3_fp04 fasta (11/19/2008) excel
nan1f1_summary   excel (4/1/2009)
nan1f2_summary   excel (4/1/2009)
nan1f2_summary   excel (4/1/2009)
nan1f3_fp03 fasta (9/28/2011) No Results



 

 

Nereocystis luetkeana

Name Nereocystis luetkeana
Class Phaeophycea, NCBI Taxonomy
Size Up to 36 m
Morphology Macroalga
Toxic
No
Regime Shallow, open, coastal waters
Strain Source UWCC MA 708




Fosmid Ends

Nereocystis luetkeana Fosmid Ends

Fosmid Plate
Raw End Sequences Best Blast Results
ner1f1_fp01
Fasta Excel (3/8/07)
ner1f1_fp03 Fasta Excel (4/3/07)
ner1f1_fp04 Fasta Excel (4/3/07)
ner1f1_fp05 Fasta
Excel (3/11/08)
ner1f1_fp06 Fasta Excel (3/11/08)

Ochromonas danica

Name Ochromonas danica
Class Chrysophyceae, NCBI Taxonomy
Size

Length: 8 - 10 µm

Width: 5 - 7 µm

Morphology Unicellular, flagellate
Toxic
No
Regime Freshwater streams
Strain Source CCMP588, UTEX1298


Fosmid Ends

fosmid Plate
Raw End Sequences Best Blast Results
ocr1f1fp01x2 Fasta (7/16/09)
No Results


AttachmentSize
ocr1f1fp01x2.fasta88.66 KB

Odontella sinensis

Courtesy of CCMP

Name Odontella sinensis
Class Coscinodiscophyceae, NCBI Taxonomy
Size

Length: 240 - 320 µm

Width: 28 - 32 µm

Morphology Unicellular
Toxic
No
Regime North Atlantic, Narragansett Bay
Strain Source CCMP1815


The marine centric diatom Odontella sinensis was the first stramenopile chloroplast genome to be completely sequenced. The circular genome is 119,704 bp in length. It contains an inverted repeat sequence of 7,725 bp separating two single-copy regions of 38,908 and 65,346 bp, respectively, and 174 genes and open reading frames, of which nine are duplicated within the inverted repeat segments.

Odontella genome pic
hetersigma bullet

References

Comparison of gene arrangements of chloroplasts between two centric diatoms, Skeletonema costatum and Odontella sinensis
Tada N, Shibata S, Otsuka S, Namba K, Oyaizu H
DNA SEQUENCE
10 (4-5): 343-347 1999

The chloroplast genome of a chlorophyll a+c-containing alga, Odontella sinensis
Kowallik KV, Stoebe B, Schaffran I, KrothPancic P, Freier U
Plant Molecular Biology Reporter
13 (4): 336-342 DEC 1995

Sequences & Annotations

Odontella sinensis

 

Downloadable Sequences and Annotated Sequences


 

 

Sequence Name Raw nt Sequence Annotated genbank Annotated embl
PDF Figure
Whole Genome
fasta
genbank
embl
pdf


This Chloroplast was not sequenced or annotated in our lab. We present these data for the sake of convenience.

Reference:

The Chloroplast Genome of a Chorophyll a+c-Containing Alga, Odontella sinensis

KV Kowaik, B Stoebe, I Schaffran, P Kroth-Pancic, and U Freier

PLANT MOLECULAR BIOLOGY REPORTER

13: 336-342 1995

Pelagomonas calceolata

Courtesy of CCMP

Name
Pelagomonas calceolata
Class
Pelagophyceae, NCBI Taxonomy
Size

Length: 2 - 4 µm

Width: 1 - 3 µm

Morphology
Unicellular, flagellated
Toxic
No
Regime
Open Ocean, Pacific
Strain Source CCMP1756

Fosmid Ends

fosmid Plate
Raw End Sequences Best Blast Results
peca1f2_fp01
Fasta (8/21/08)
Excel
peca1f2_fp02 Fasta (8/21/08)
Excel


Sequences & Annotations

Phaeothamnion confervicola

Courtesy of CCMP

Name
Phaeothamnion confervicola
Class
Phaeothamniophyceae, NCBI Taxonomy
Size

Length: 8 - 15 µm

Width: 4 - 7 µm

Morphology
Unicellular, branched
Toxic
No
Regime
Freshwater, Europe
Strain Source CCMP637

Fosmid Ends

fosmid Plate
Raw End Sequences Summary
phae1f1_fp01
Fasta (7/28/08)
Excel
phae1f1_fp02 Fasta (7/28/08) Excel


Pinguiococcus pyrenoidosus

Courtesy of CCMP

Name Pinguiococcus pyrenoidosus
Class Pinguiophyceae, NCBI Taxonomy
Size

Length: 3 - 10 µm

Width: 3 - 8 µm

Morphology Unicellular, coccoid
Toxic
No
Regime North Atlantic
Strain Source CCMP2188


Pinguiococcus pyrenoidosus (Pinguiophyceae) is a yellow-brown alga in the heterokont (aka stramenochromes) group. It is the only identified species of the genus. It is small coccoid marine alga with a single chloroplast having a typical photosynthetic stramenopile ultrastructure and vacuoles cotaning a large percentage of eicosapentaenoic acid.

Its pigmentation and plastid ultrastructure, flagellar apparatus and small-subunit rRNA (SSU rRNA) have been well characterized in order to determine its phylogenetic position and relationship to the different groups of algae, and in particular its relationship among the different classes of heterokont algae. Little is known about its chloroplast genome.

 

Fosmid Ends

Pinguiococcus pyrenoidosus



Fosmid End Sequences



Fosmid Plate Raw End Sequences Full Blast Results
(big files)
Best Blast Results
pinf1 fp01 and fp02
fasta
  best.xls
pin1f1 fp04
fasta
Raw Blast
best.xls
pin1f1 fp06
fasta RawBlast best.xls (05/23/07)

Pleurochloridella botrydiopsis

Courtesy of CCMP

Name
Pleurochloridella botrydiopsis
Class
Phaeothamniophyceae, NCBI Taxonomy
Size

Length: 5 - 8 µm

Width: 5 - 8 µm

Morphology
Unicellular
Toxic
No
Regime
South Pacific
Strain Source CCMP1665

Fosmid Ends

Pleurochloridella botrydiopsis

Fosmid End Sequences


 

Fosmid plate Raw sequence Best Blast Results
pleu1f1_fp01 Fasta Excel (9/24/08)
pleu1f1_fp02 Fasta Excel (9/24/08)
pleu1f1_fp03 Fasta Excel (9/24/08)

 

 

 

 

 

Pseudocharaciopsis minuta

Name
Pseudocharaciopsis minuta
Class
Eustigmatophyceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Strain Source UTEX 2113

Rhizochromulina marina

Courtesy of CCMP

Name
Rhizochromulina marina
Class
Dictyochophyceae, NCBI Taxonomy
Size

Length: 4 - 8 µm

Width: 4 - 8 µm

Morphology
Unicellular
Toxic
No
Regime
North Atlantic, Sargasso Sea, Open ocean
Strain Source
CCAP950/1

Fosmid Ends

Fosmid plate Raw sequence Best Blast Results
rhiz1f1_fp01 Fasta Excel (3/11/08)
rhiz1f1_fp02 Fasta
Excel (3/11/08)
rhiz1f1_fp03 Fasta
Excel (4/17/08)
rhiz1f1_fp04 Fasta
Excel (4/17/08)

Schizocladia ischiensis

Courtesy of CCMP

Name
Schizocladia ischiensis
Class
Schizocladiophyceae, NCBI Taxonomy
Size

Length: 10 - 24 µm

Width: 3 - 7 µm

Morphology
Unicellular, branched
Toxic
No
Regime
North Atlantic, Mediterranean Sea
Strain Source CCMP2287

Fosmid Ends

fosmid Plate
Raw End Sequences Best Blast Results
scis1f2_fp01
Fasta (8/6/08)
Excel
scis1f2_fp02 Fasta (8/21/08)
Excel


Synchroma grande

Courtesy of CCMP

Name
Synchroma grande
Class
Synchromophyceae, NCBI Taxonomy
Size

Length: 28 - 20 µm

Width: 18 - 25 µm

Morphology
Unicellular
Toxic
No
Regime
North Atlantic
Strain Source CCMP2876

Fosmid Ends

fosmid Plate
Raw End Sequences Best Blast Results
sygr1f2_fp01
Fasta (12/11/08)
Excel
sygr1f2_fp02
Fasta (12/11/08)
Excel


Synura petersenii

Name Synura petersenii
Class Synurophyceae, NCBI Taxonomy
Size

Length: 13 - 25 µm

Width: 10 - 13 µm

Morphology Unicellular, flagellate colony
Toxic
No
Regime Freshwater
Strain Source CCMP854


Synura petersenii belongs to the class Synurophyceae. This class has about 150 species of silica-scaled algae (Andersen and Preisig 2002a)

Synura petersenii . The 91.5 kb chloroplast genome of this alga has been partially characterized (Wee et al. 1993). This oligotrophic, freshwater alga is a nuisance species in that it produces volatile organic compounds that impart an unpleasant taste and odor to drinking water (Watson et al. 2001).






References:

Andersen, R. A. and H. Preisig (2002a).
Synurophyceae. in An Illustrated Guide to the Protozoa: 2nd Ed. P. C. Bradbury, eds. Society of Protozoologists, Lawrence, KS. pp. 759-775.

Watson, S. B., T. Satchwill, E. Dixon and E. McCauley (2001). Under-ice blooms and source-water odor in a nutrient-poor reservoir: biological, ecological and applied perspectives. Fresh Water Biol. 46: 1553-1567

Wee, J., J. Chesnick and R. A. Cattolico (1993). Partial characterization of the chloroplast genome from the chromophytic alga Synura petersenii (Synurophyceae). J. Phycol. 29: 96-99.

Fosmid Ends

Synura petersenii

Fosmid End Sequences


Fosmid Plate
Raw End Sequences Best Blast Results
syn1f1_fp01 syn1f1_fp01 Excel
syn1f1_fpo2 syn1f1_fpo2 Excel
syn1f1_fp04
syn1f1_fp04 (02/27/07) Excel
syn1 f1_fp05
syn1f1_fp05 (05/23/07) Excel
syn1 f1_fp03 syn1f1_fp03 (06/14/07) Excel
syn1 f1_fp06 syn1 f1_fp06 (06/21/07) Excel
syn1 f2_fp01 fasta (4/15/08) No Results
syn1 f2_fp02 fasta (4/23/08) Excel
syn1 f2_fp03 fasta (5/29/08) Excel
syn1 f2_fp04 fasta (5/29/08) Excel
syn1 f2_fp05 fasta
Excel
syn1 f2_fp06 fasta Excel
syn1 f2_fp03x2 fasta (8/18/08)
Excel
syn1 f2_fp04x2 fasta (8/18/08) Excel
syn1 f3_fp01 fasta (10/6/08)
Excel
syn1 f3_fp02 fasta (10/6/08)
Excel
syn1_f1_summary Excel (2/19/09)
syn1_f2_summary Excel (2/19/09)
syn1_f3_summary Excel (2/19/09)


Syringoderma abyssicola

Name
Syringoderma abyssicola
Class
Phaeophyceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Strain Source KU-758

Tessellaria volvocina

Courtesy of CCMP

Name
Tessellaria volvocina
Class
Synurophyceae, NCBI Taxonomy
Size

Length: 18 - 50 µm

Width: 5 - 9 µm

Morphology
Unicellular, colonial, flagellated
Toxic
No
Regime
Freshwater
Strain Source CCMP1781

Fosmid Ends

Fosmid plate Raw sequence Best Blast Results
tevof1_fp01 Fasta Excel (5/13/08)
tevof1_fp02 Fasta
Excel (5/13/08)

 

 

 

 

Sequences & Annotations

Tetrasporopsis fuscescens

Name
Tetrasporopsis fuscescens
Class
Phaeothamniaceae, NCBI Taxonomy
Size
Morphology
Toxic
Regime
Freshwater
Strain Source SAG2088

Fosmid Ends

Fosmid plate Raw sequence Best Blast Results
tefuf2_fp01 Fasta Excel (5/13/08)
tefuf2_fp02 Fasta
Excel (5/13/08)

Thalassiosira pseudonana

Courtesy of CCMP

Name Thalassiosira pseudonana
Class Coscinodiscophyceae, NCBI Taxonomy
Size

Length: 4 - 6 µm

Width: 4 - 5 µm

Morphology Unicellular
Toxic
No
Regime North Atlantic
Strain Source CCMP1335


The entire genome, including the chloroplast, of the marine centric diatom Thalassiosira pseudonana is being sequenced at the Department of Energy's Joint Genome Institute. Thalassiosira pseudonana was chosen as the first eukaryotic marine phytoplankton for whole genome sequencing because this species has served as a model for diatom physiology studies, and the nuclear genome is relatively small (34 Mbp).




hetersigma bullet

References:

The genome of the diatom Thalassiosira pseudonana: Ecology, evolution and metabolism.
Armbrust, EV, JA Berges, C Bowler, BR Green, D Martinez, NH Putnam, S Zhou, AE Allen, KE Apt, M
Bechner, MA Brzezinski, BK Chaal, A Chiovitti, AK Davis, MS Demarest, J C Detter, T Glavina, D Goodstein, MZ Hadi, U Hellsten, M Hildebrand, BD Jenkins, J Jurka, VV Kapitonov, N Kröger, WWY Lau, TW Lane, FW Larimer, JC Lippmeier, S Lucas, M Medina, A Montsant, M Obornik, MS Parker, B Palenik, GJ Pazour, PM Richardson, TA Rynearson, MA Saito, DC Schwartz, K Thamatrakoln, K Valentin, A Vardi, FP Wilkerson, and DS Rokhsar.
SCIENCE
306: 79-86 2004

Effects of temperature, nitrogen, and light limitation on the optical properties of the marine diatom Thalassiosira pseudonana
Stramski D, Sciandra A, Claustre H
LIMNOLOGY AND OCEANOGRAPHY
47 (2): 392-403 MAR 2002

Effects of temperature on growth rate, cell composition and nitrogen metabolism in the marine diatom Thalassiosira pseudonana (Bacillariophyceae)
Berges JA, Varela DE, Harrison PJ
MARINE ECOLOGY PROGRESS SERIES
225: 139-146 2002

Rapid evolution of a sexual reproduction gene in centric diatoms of the genus Thalassiosira
Armbrust EV, Galindo HM
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
67 (8): 3501-3513 AUG 2001

Response of growth and biochemical composition to variations in daylength, temperature, and irradiance in the marine diatom Thalassiosira pseudonana (Bacillariophyceae)
Thompson P
JOURNAL OF PHYCOLOGY
35 (6): 1215-1223 DEC 1999

Sequences & Annotations

Thalassiosira pseudonana

 

Downloadable Sequences and Annotated Sequences


 

 

Sequence Name Raw nt Sequence Annotated genbank Annotated embl
PDF Figure
Whole Genome
fasta
genbank
embl

pdf

pdf - with repeats


This Chloroplast was not sequenced or annotated in our lab. We present these data for the sake of convenience.

Tribonema aequale

Name
Tribonema aequale
Class
Xanthophyceae, NCBI Taxonomy
Size

Length: 8 - 14 µm

Width: 4 - 5 µm

Morphology
Unicellular, branched
Toxic
No
Regime
Freshwater
Strain Source CCMP1275

Fosmid Ends

Fosmid plate Raw sequence Best Blast Results
trif1_fp01 Fasta Excel (8/23/07)
tri1f1_fp02 Fasta
Excel (9/21/07)
tri1f1_fp03 Fasta Excel (3/11/08)
tri1f1_fp04 Fasta
Excel (3/11/08)

 

 

 

 

Vaucheria litorea

Courtesy of CCMP

Name
Vaucheria litorea
Class
Vaucheriaceae, NCBI Taxonomy
Size
40 - 50 µm
Morphology
Toxic
No
Regime
Strain Source


hetersigma bullet

References:

Solar-Powered Sea Slugs. Mollusc/Algal Chloroplast Symbiosis

Rumpho ME, Summer EJ, Manhart JR

PLANT PHYSIOLOGY

123: 29-38 MAY 2000

Sequences & Annotations