Amphidinium carterae CCMP1314

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Environmental Data
Principle Investigator(s)	Senjie Lin
External sample ID	AmpcaSL1
NCGR Sample ID	MMETSP0398C
Sample accession number	CAM_SMPL_002537
Assembly accession number	CAM_ASM_000355
Combined Assembly Name	Amphidinium-carterae-CCMP1314
Genus	Amphidinium
Species	carterae
Strain	CCMP1314
Clonal	Yes
Axenic	No
Prelim. NCBI Taxon ID	2961
18S rRNA	AGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGCATAAGCGATCTTCAGCAAGGCTGCAAA TGGCTCATTACAACAGCAATAATTTTCGCAGTGCTTCATCGCACATGGATAACTGTGGAAAATCTAGGGC TAATACATGCGTCATACCTGACTTCTGGGAAAGGTTGCTATCATGAGTCATAGAATCGGCGCAGGCTCTG CCTTGCTACCAAGGTGAGTCATGATAATTTAGCTGATCGCATTGCATCAGCTGGTGATGAACTGCACAAG TTTCTGACCTATCAGCTTCCGACGCTAGGGTATTGGCCTACTGTGGCAATGACGGGTGACGGAGAATTAG GGTTCGATTCCGGAGAGGGAGCCTGACACATGGCTACCACATCTAAGGAAGGCAGCAGGCGCGCAAATTA CCCAATCCTGACATGGGGAGGTAGTGACAAGCAATAACAATACGGGGCATCCATGTCTTGTAATTGGAAT GAGCTAACTGTAAACATGTTGGTGAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTC CAGCTCCAATAGCGTATATTAAAGCTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCAAGTACAAC TGGTCCGCCCTCTGGGTGAGCACATAGTTTGGTCTTGGCATCTTGCTGGAAACTGTTGCTGCACTTGGCT GTGTGGCGCAGTGTCCAGCACTTTCACTTTGAGGAAATTGGAGTGTTTCAAGCAGGCAATGCCTTTGAAC ACAGTAGCATGGAATAATTAGATTGGGCTTTTGCTCCAATTTGTCGGTTTCTGGAGCTGAGGTGAGAATT AATGGGGATTGTTGGGGGCATCCGAATTCAGCCGTCAGAGGTGAAATTCTTGGATCGGCTAAAGACGGAC AACTGCGAAAGCGTTTGCCCAGGATGTTTTCATTGATCAAGAACGAAAGTTAGGGGATCGAAGACGATCA GATACCGTCCTAGTCTTAACCATAAACTATGCCAACTAGGGATTGGTGGTCGTTAGTTGCACGACCCCAT CAGCACCTGATGAGAAATCAAAGTCTTTGGGTTCTGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGG AATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCA GGTCCAGACATAGGTAGGATCGACAGATTGATAGCTCTTTCGTGATTCTATGGGTGGTGGTGCATGGCCG TTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTTATCTGGCTAAGTAGCT ATGCATAGCTGTGGTTCTGTGGACAGTTTCTTAGAGGGACTTCGTGCGCCTAGCATGAGGAAGTTTGAGG CAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCTGCACGCGCGCTACACTGATACCTTCAGCGAGT CCACCACCTTGCCTGGGAGGGTGGGGTAACCTCTGGAAAGTGCATCGTGATGGGGATCGATTATTGTAAT TATTAATCTTCAACGAGGAATTCCTAGTAAGCATGTGTCATCAGCCCGTGCTGATTACGTCCCTGCCCTT TGTACACACCGCCCGTCGCTCCTACCGATTGAGTGATCCGGTGAATTATTCGGACTGCAACGCGTTCAGT CTCTGTATGCTGTTGCGGAAAGTTTTGTGAACCTTACCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTT CC
Importance of organism and transcriptomes	Compared to the other dinoflagellate species we nominated by this group of researchers, Amphidinium carterae has the following unique characteristics that makes it of high interest to sequence its genome-wide trasncriptome, 1) similar genome size (~3 gb) and similarly basal position in dinoflagellate phylogeny as Symbiodinium kawagutii, 2) free-living (unlike S. kawagutii), 3) produces toxins (unlike S. kawagutii), but the toxins are polyketide type (unlike toxins from Alexandrium), but different from the polyketide toxin produced by Karenia brevis, 4) photosynthetic with peridinin-containing plastid, 5) some EST data has been done, mainly full-length cDNA clones (~20,000 total clones, generated in the PI?s laboratory), which can be very useful templates for assembly of Illumina reads being proposed.
Additional citations and references
Primary citation for organism's characterization, if available	Zhang, H., Bhattacharya, D. and Lin, S. 2007. A three-gene dinoflagellate phylogeny suggests monophyly of Procentrales and a basal positon for Amphidinium and Heterocapsa. J. Mol. Evol. 65: 463-474.
Latitude	41.56
Longitude	70.583
Sample collection site	Atlantic_Ocean
Other collection site info	Falmouth Great Pond, Falmouth, Massachusetts
Habitat	marine habitat
Country	UNITED STATES
Experimental Data
Date of experiment	15-MAY-11
Growth medium	f/2 amended seawater
Temperature (ºC)	20
Salinty (psu)	28
pH	8.1
Light (µmol photons / m2 / sec)	200
Day portion of day:night cycle in hours	14
Night portion of day:night cycle in hours	10
Nitrate (μmol/L)	882
Phosphate (μmol/L)	36.2
Trace elements (total) (nmol/L)	11.7
Investigation type	Eukaryotes
Other experimental metadata available	submitted is dinoflagellate spliced leader based cDNA prepared when culture was enriched in G1 phase.