Dataset: ITS_sequence_accessions
Deployment: lab_Rynearson_diatoms

Summary of methods: Thalassiosira rotula and Thalassiosira gravida
See Whittaker et al. (2012) for more information. Cells of the diatom Thalassiosira rotula/gravida were collected from the Eastern and Western Pacific and from the Western Atlantic between 2007 and 2009. Cultured isolates were also obtained (refer to Table 1 of Whittaker et al. (2012)). Three regions of the ribosomal DNA (rDNA) were sequenced: the small subunit (18S), the D1 hypervariable region of the large subunit (28S), and the internal transcribed spacer region I (ITS1). ITS1 was amplified from 106 isolates by polymerase chain reaction (PCR) using a newly-designed primer specific to T. rotula and T. gravida and primer 1645F. The 18S was amplified from 16 isolates using universal 18SA and 18SB primers. The D1 region of the 28S was also amplified from those 16 isolates using the forward primer 28SF and a reverse primer. Sequencing was performed on an ABI 3130xl (Applied Biosystems). SeqMan II 3.61 (DNASTAR, Inc.) was used to assemble sequences and they were aligned using Clustal W in Mega4. Boundaries of the ITS1 were determined through alignment with Genbank accession EF208798.

Refer to Rynearson et al. (2009) for the Ditylum brightwellii methodology.

References:
Rynearson, T.A., E.O. Lin and E.V. Armbrust. 2009. Metapopulation structure in the planktonic diatom Ditylum brightwellii (Bacillariophyceae). Protist, 160(1):111-121. doi:10.1016/j.protis.2008.10.003

Whittaker, K., Rignanese, D., Olson, R., Rynearson, T., 2012. Molecular subdivision of the marine diatom Thalassiosira rotula in relation to geographic distribution, genome size, and physiology. BMC Evolutionary Biology, 12:209. doi:10.1186/1471-2148-12-209