The amplifications were done on an Eppendorf Mastercycler ep (Eppendorf, Germany) and a Biometra Thermocycler (Biometra, Germany) with a sample volume of 25 μl containing 10 – 200 ng of template DNA, 1 × HotMaster Taq Buffer with
2.5 mM Mg2+ (5 Prime, USA), 200 μM dNTPs, 0.2 μM of each primer and 1.5 U HotMaster Taq DNA Polymerase (5 Prime, USA). The reaction mixture was incubated at 94°C for 2 min, followed by 30 – 34 cycles of 45 s at 94°C, 45 s at 60°C, 135 s at 72°C with a final extension at 72°C for 10 min. The PCR products were gel-extracted and purified using Wizard SV Gel and PCR Clean-Up System (Promega, USA), and cloned using TOPO TA Cloning Kit (Invitrogen, USA) following the manufacturers instructions. ARRY-438162 price Colonies were checked for positive inserts by PCR amplification with the primers 4EGI-1 cell line TopoF (5′-GGCTCGTATGTTGTGTGGAATTGT-3′) and TopoR (5′-CCGTCGTTTTACAACGTCGTGACT-3′) and SRT2104 identical reaction mixtures as described above, except that DynaZymeII (Finnzymes, Finland) DNA polymerase (1.5 U) and 1 × DynaZyme buffer (F-511) were used. The PCR program was as follows: Initial denaturation at 95°C for 5 min, 34 cycles of 15 s at 95°C, 30 s at 60°C, 120 s at 72°C with a final extension at 72°C for 7 min. The positive inserts were sequenced on an ABI 3730 DNA Analyzer (Applied Biosystems,
USA) with the primers M13F and M13R (Invitrogen, USA) using the ABI BigDye terminator v3.1 kit (Applied Biosystems, USA). 183 clones were randomly picked from the generated libraries and sequenced with the M13F primer (Invitrogen, USA). Identical, or nearly identical, sequences were not sequenced further. 82 of the inserts were full-length sequenced (approximately 1500 bp) with the M13R primer (Invitrogen, USA). Accession numbers for sequences generated in this study [GenBank: GQ365764-GQ365903 and GU117661-GU117693]. Figure 2 Primers used in this study and their relative position in 18S
rDNA gene. * indicates that primer is based on PrimerA and ** indicates that primer is based on PrimerB designed by Medlin et al. . The 18S Methane monooxygenase rDNA gene in the figure is based on the Telonema antarcticum sequence AJ564773 (1787 bp) in GenBank . Phylogenetic analyses Available sequences of possible Telonemia origin were identified by BLAST searches against the Entrez Nucleotide database [61, 62] using sequences of known Telonemia origin as query. The sequences identified from the BLAST searches were downloaded and pooled into a local database together with the sequences generated in this study. These sequences were added to an 18S rDNA alignment of all the major eukaryotic groups (hereafter called alignment 1) to confirm relationship to Telonemia. After removal of ambiguously aligned characters using the program MacClade version 4.07 , alignment 1 consisted of 374 taxa and 1465 characters. Alignment 1 was subjected to maximum likelihood (ML) analyses by using the program RAxML v.