Computational protocol: Characterization and robust nature ofnewly isolated oleaginous marine yeast Rhodosporidium spp. from coastal water of Northern China

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Protocol publication

[…] Yeast isolates were identified by sequence analysis of 18S rRNA gene. Total genomic DNA of yeast cells was extracted using DNA extraction kit (Generay, China), following the manufacturer’s instruction. The 18S rRNA gene fragment was amplified by polymerase chain reaction (PCR) in the S1000™ Thermal cycler (Bio-Rad, USA) with the fungi universal primers, EF4 (5′-GGAAGGG (G/A) TGTATTTATTAG-3′) and EF3 (5′-TCCT (A/C) TAAATGACCAAGTTTG-3′) (Smit et al. ). The PCR reaction was carried out under the initial denaturation at 94 °C for 5 min, followed by 30 cycles of 30 s at 94 °C, 30 s at 51 °C and 90 s at 72 °C, and a final extension at 72 °C for 10 min. The PCR products were purified using Gel DNA extraction kit (Generay, China). The resulting PCR products were sequenced at Beijing Genomics Institute (China) and the final sequences were edited using BioEdit and then compared with the National Center for Biotechnology Information database. Phylogenetic analyses were carried out using distance setting (Maximum likelihood) in MEGA 6 software with 1000 bootstrap replicates (Tamura et al. ). The 18S rRNA gene sequences obtained for this study were submitted to GenBank under the access number of KU317620-317626 and KT281890-281892. […]

Pipeline specifications

Software tools BioEdit, MEGA
Application Phylogenetics
Organisms Saccharomyces cerevisiae
Chemicals Fatty Acids, Glucose, Oleic Acid, Palmitic Acid, Linoleic Acid