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

Abstract

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.

Keywords

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

Published in

Genomics
2021, volume: 113, number: 6, pages: 4022-4027
Publisher: ACADEMIC PRESS INC ELSEVIER SCIENCE

SLU Authors

• Martín Hernández, Giselle De La Caridad

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Müller, Bettina

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Chmielarz, Mikolaj

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Passoth, Volkmar

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Genetics and Genomics

Publication identifier

• DOI: https://doi.org/10.1016/j.ygeno.2021.10.006

Permanent link to this page (URI)

https://res.slu.se/id/publ/114296