Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage



Barbitoff, Yury A, Matveenko, Andrew G, Matiiv, Anton B, Maksiutenko, Evgeniia M, Moskalenko, Svetlana E, Drozdova, Polina B, Polev, Dmitrii E, Beliavskaia, Alexandra Y ORCID: 0000-0002-1194-5689, Danilov, Lavrentii G, Predeus, Alexander V ORCID: 0000-0002-2750-1599
et al (show 1 more authors) (2021) Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage. G3-GENES GENOMES GENETICS, 11 (4). jkab029-.

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Abstract

Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.

Item Type: Article
Uncontrolled Keywords: Yeast genome, 74-D694, long reads, structural variant, FLO genes
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 17 May 2021 09:38
Last Modified: 18 Jan 2023 22:46
DOI: 10.1093/g3journal/jkab029
Open Access URL: https://doi.org/10.1093/g3journal/jkab029
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3123026