Computational Biology
@ Comenius University in Bratislava

Brona Brejova, Viktoria Hodorova, Sofia Mutalova, Andrea Cillingova, Lubomir Tomaska, Tomas Vinar, Jozef Nosek. Chromosome-level genome assembly of the yeast Lodderomyces beijingensis reveals the genetic nature of metabolic adaptations and identifies subtelomeres as hotspots for amplification of mating type loci. DNA Research, 31(3). 2024.

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Download from publisher: https://doi.org/10.1093/dnares/dsae014

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Abstract:

Lodderomyces beijingensis is an ascosporic ascomycetous yeast. In contrast to 
related species Lodderomyces elongisporus, which is a recently emerging human 
pathogen, L. beijingensis is associated with insects. To provide an insight into 
its genetic makeup, we investigated the genome of its type strain, CBS 14171. We 
demonstrate that this yeast is diploid and describe the high contiguity nuclear 
genome assembly consisting of eight chromosome-sized contigs with a total size of 
about 15.1 Mbp. We find that the genome sequence contains multiple copies of the 
mating type loci and codes for essential components of the mating pheromone 
response pathway, however, the missing orthologs of several genes involved in the 
meiotic program raise questions about the mode of sexual reproduction. We also 
show that L. beijingensis genome codes for the 3-oxoadipate pathway enzymes, 
which allow the assimilation of protocatechuate. In contrast, the GAL gene 
cluster underwent a decay resulting in an inability of L. beijingensis to utilize 
galactose. Moreover, we find that the 56.5 kbp long mitochondrial DNA is 
structurally similar to known linear mitochondrial genomes terminating on both 
sides with covalently closed single-stranded hairpins. Finally, we discovered a 
new double-stranded RNA mycovirus from the Totiviridae family and characterized 
its genome sequence.