DNA was isolated from the sample LP01 with a DNeasy Plant Mini Kit (Qiagen). Cells were mechanically disrupted by shaking for 15 min (30 Hz) in the presence of glass beads (3 mm diameter, Sigma–Aldrich) in a Mixer Mill MM 400 (Retsch, Germany). Then, samples were put in freezer at −20 °C for half an hour. Subsequently, DNA was isolated in accordance with the manufacturer’s procedure. Quality and concentration of DNA was measured on the NanoDrop
® ND–1000 Spectrophotometer (NanoDrop Technologies, Inc.).
The 18S small subunit ribosomal RNA gene (18S rDNA), internal transcribed spacer regions 1 and 2 (ITS1, ITS2 rDNA) and ribulose–1,5–bisphosphate carboxylase/oxygenase large subunit (
rbcL) gene regions were amplified from DNA isolates by PCR using existing primers (
Table 2). Amplification reactions for 18S rDNA was performed using cycle parameters according to Katana et al. (2001) with minor modification that duration of initial denaturation was prolonged for 10 min and annealing temperatures were 50 °C, 58 °C and 61 °C. Amplification reactions for
rbcL gene were performed using cycle parameters according to Hoham et al. (2002) with minor change that three different annealing temperatures were applied (53 °C, 55 °C, 59 °C). Each 20 μl of PCR reaction for 18S and
rbcL amplification contained 5 μl of DNA isolates (diluted to concentration of 5 ng.μl
−1), 0.8 μl of each 10 μM primer, 1.6 μl of 25 mM MgCl
2, 1.5 μl of 2 mM dNTPs, 2 μl of 10× Taq buffer + KCl–MgCl
2, 7.8 μl sterile Milli–Q water, and 0.5 μl of 1U.μl
−1 Taq DNA polymerase (Fermentas, USA). Amplification reactions for ITS2 rDNA region were performed using cycle parameters according to Goff & Moon (1993) with minor modification that the gradient of annealing temperature was included (56 °C, 58 °C, 61 °C, 64 °C). Each 35 μl PCR reaction contained 1 μl of DNA isolates (diluted to concentration of 5 ng μl
−1), 1.4 μl of each 10 μM primer, 2.8 μl of 25 mM MgCl
2, 2.6 μl of 2 mM dNTPs, 3.5 μl of 10× buffer Taq buffer + KCl–MgCl
2, 21.8 μl sterile Milli–Q water, and 0.5 μl of 1U.μl
−1 Taq DNA polymerase (Fermentas). The PCR products were stained with bromophenol loading dye, quantified on 1.5% agarose gel, stained with GelRed. The amplification products were purified and sequenced using an Applied Biosystems automated sequencer (ABI 3730×l) at Macrogen (Korea). The newly obtained sequences were submitted to NCBI Nucleotide sequence database (accession numbers for
Cr. nivalis subsp.
tatrae LP01: 18S, ITS1, ITS2 – KY499614, rbc
L – KY499615;
Cr. nivalis P24/DR4: rbc
L – KY499616).
The nuclear rDNA ITS2 region was identified using a web interface at the ITS2 database showing position of 5.8S and 26S motives (
http://its2.bioapps.biozentrum.uni–wuerzburg.de/cgi–bin/index.pl?annotator; Koetschan et al. 2010 (
link)). The sequence was then folded with 5.8S–LSU stem regions using the Mfold server accessible at
http://mfold.rna.albany.edu/?q5mfold (Zuker 2003 (
link)). A model of the secondary structure consistent with the specific features of nuclear rDNA ITS2 was selected: four helixes, U–U mismatch in helix II, and the UGGU motif near the 5´–end site apex of helix III (Coleman 2007 (
link)).
Procházková L., Remias D., Řezanka T, & Nedbalová L. (2017). Chloromonas nivalis subsp. tatrae, subsp. nov. (Chlamydomonadales, Chlorophyta): re–examination of a snow alga from the High Tatra Mountains (Slovakia). Fottea (Praha), 18(1), 1-18.