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

Martín Hernández, Giselle De La Caridad and Müller, Bettina and Chmielarz, Mikolaj and Brandt, Christian and Hoelzer, Martin and Viehweger, Adrian and Passoth, Volkmar (2021). Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14. Genomics. 113 , 4022-4027
[Research article]

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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.

Authors/Creators:Martín Hernández, Giselle De La Caridad and Müller, Bettina and Chmielarz, Mikolaj and Brandt, Christian and Hoelzer, Martin and Viehweger, Adrian and Passoth, Volkmar
Title:Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14
Series Name/Journal:Genomics
Year of publishing :2021
Volume:113
Page range:4022-4027
Number of Pages:6
Publisher:ACADEMIC PRESS INC ELSEVIER SCIENCE
ISSN:0888-7543
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
Keywords:Rhodotorula toruloides, de-novo hybrid assembly, Nanopore sequencing, Annotation
URN:NBN:urn:nbn:se:slu:epsilon-p-114296
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-114296
Additional ID:
Type of IDID
DOI10.1016/j.ygeno.2021.10.006
Web of Science (WoS)000710919300004
ID Code:26092
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Molecular Sciences
Deposited By: SLUpub Connector
Deposited On:11 Nov 2021 15:25
Metadata Last Modified:11 Nov 2021 15:31

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