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Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence

Martín Hernández, Giselle De La Caridad and Müller, Bettina and Brandt, Christian and Hoelzer, Martin and Viehweger, Adrian and Passoth, Volkmar (2022). Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence. Journal of Fungi. 8 :4 , 323
[Research article]

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Abstract

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorula babjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058, at chromosomal level. Both genomes are 21 Mbp in size and have a GC content of 68.2%. Allele frequency analysis indicates that both strains are tetraploid. The genomes consist of a maximum of 21 chromosomes with a size of 0.4 to 2.4 Mbp. In both assemblies, the mitochondrial genome was recovered in a single contig, that shared 97% pairwise identity. Pairwise identity between most chromosomes ranges from 82 to 87%. We also found indications for strain-specific extrachromosomal endogenous DNA. A total of 7591 and 7481 protein-coding genes were annotated in CBS 7808 and DBVPG 8058, respectively. CBS 7808 accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes. Genome divergence values between the two strains indicate that they may belong to different species.

Authors/Creators:Martín Hernández, Giselle De La Caridad and Müller, Bettina and Brandt, Christian and Hoelzer, Martin and Viehweger, Adrian and Passoth, Volkmar
Title:Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence
Series Name/Journal:Journal of Fungi
Year of publishing :2022
Volume:8
Number:4
Article number:323
Number of Pages:19
Publisher:MDPI
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) > Microbiology (Microbiology in the medical area to be 30109)
Keywords:Rhodotorula babjevae, de novo hybrid assembly, nanopore sequencing, genome divergence, ploidy
URN:NBN:urn:nbn:se:slu:epsilon-p-117017
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-117017
Additional ID:
Type of IDID
DOI10.3390/jof8040323
Web of Science (WoS)000786004100001
ID Code:28278
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Molecular Sciences
Deposited By: SLUpub Connector
Deposited On:08 Jun 2022 15:30
Metadata Last Modified:08 Jun 2022 15:31

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