Sequencing and Assembly of Rhodotorula kratochvilovae Genome

Total DNA of R. kratochvilovae strain YM25235 was extracted using Wizard Genomic DNA Purification Kit (Promega, Madison, WI, United States). The next experimental procedures were performed according to the standard protocols provided by Oxford Nanopore Technologies (ONT). To optimize the sequencing experiments and improve the throughput, a library was constructed using the SQK-LSK109 Ligation Sequencing Kit. Then, the library was sequenced on the Nanopore PromethION platform. After sequencing, the downstream sequencing data were analyzed by basecalling programs using the Albacore software from the MinKNOW package to convert the raw sequencing data from FAST5 format to FASTQ format (Wick et al., 2019 (link)). Further filtering for the adaptor, low quality, and short reads (<2,000 bp in length) resulted in total dataset clean reads. Canu v1.5 software was used to correct the filtered subreads (Koren et al., 2017 (link)). Next, we assembled the subreads after error correction using the wtdbg software to obtain the final genome with high accuracy (Ruan and Li, 2019 (link)). The BUSCO v2.0 software was used to assess the completeness of the R. kratochvilovae strain YM25235 genome assembly (Simão et al., 2015 (link)).