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Martín-Hernández, Giselle C. [Author]; Müller, Bettina [Author]; Brandt, Christian [Author]; Hölzer, Martin [Author]; Viehweger, Adrian [Author]; Passoth, Volkmar [Author]

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

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  • Media type: E-Article
  • Title: Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence
  • Contributor: Martín-Hernández, Giselle C. [Author]; Müller, Bettina [Author]; Brandt, Christian [Author]; Hölzer, Martin [Author]; Viehweger, Adrian [Author]; Passoth, Volkmar [Author]
  • imprint: Basel: MDPI, [2023]
  • Published in: Fungi ; 8, (2022)
  • Language: English
  • Keywords: ploidy ; nanopore sequencing ; de novo hybrid assembly ; genome divergence ; Rhodotorula babjevae
  • Origination:
  • Footnote:
  • Description: The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorulababjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genomeassemblies 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 sizeand 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 forstrain-specific extrachromosomal endogenous DNA. A total of 7591 and 7481 protein-coding geneswere annotated in CBS 7808 and DBVPG 8058, respectively. CBS 7808 accumulated a higher numberof tandem duplications than DBVPG 8058. We identified large translocation events between putativechromosomes. Genome divergence values between the two strains indicate that they may belong todifferent species.
  • Access State: Open Access
  • Rights information: Attribution (CC BY)