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Research article2021Peer reviewedOpen access

Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14

Martin-Hernandez, Giselle C.; Muller, Bettina; Chmielarz, Mikolaj; Brandt, Christian; Hoelzer, Martin; Viehweger, Adrian; Passoth, Volkmar


Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size of the genome is 20,534,857 bp and the overall GC content is 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. We annotated 9464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.


Rhodotorula toruloides; de-novo hybrid assembly; Nanopore sequencing; Annotation

Published in

2021, Volume: 113, number: 6, pages: 4022-4027