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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.; Danilov, Lavrentii G.; Predeus, Alexander V.; Zhouravleva, Galina A.

In: G3: Genes, Genomes, Genetics, Vol. 11, No. 4, jkab029, 04.2021.

Research output: Contribution to journal › Article › peer-review

Harvard

Barbitoff, YA, Matveenko, AG, Matiiv, AB, Maksiutenko, EM, Moskalenko, SE, Drozdova, PB, Polev, DE, Beliavskaia, AY, Danilov, LG, Predeus, AV & Zhouravleva, GA 2021, 'Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage', G3: Genes, Genomes, Genetics, vol. 11, no. 4, jkab029. https://doi.org/10.1093/g3journal/jkab029

APA

Barbitoff, Y. A., Matveenko, A. G., Matiiv, A. B., Maksiutenko, E. M., Moskalenko, S. E., Drozdova, P. B., Polev, D. E., Beliavskaia, A. Y., Danilov, L. G., Predeus, A. V., & Zhouravleva, G. A. (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]. https://doi.org/10.1093/g3journal/jkab029

Vancouver

Barbitoff YA, Matveenko AG, Matiiv AB, Maksiutenko EM, Moskalenko SE, Drozdova PB et al. Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage. G3: Genes, Genomes, Genetics. 2021 Apr;11(4). jkab029. https://doi.org/10.1093/g3journal/jkab029

Author

Barbitoff, Yury A. ; Matveenko, Andrew G. ; Matiiv, Anton B. ; Maksiutenko, Evgeniia M. ; Moskalenko, Svetlana E. ; Drozdova, Polina B. ; Polev, Dmitrii E. ; Beliavskaia, Alexandra Y. ; Danilov, Lavrentii G. ; Predeus, Alexander V. ; Zhouravleva, Galina A. / Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage. In: G3: Genes, Genomes, Genetics. 2021 ; Vol. 11, No. 4.

BibTeX

@article{2263f998772d4d068c61ab98ada58a76,
title = "Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage",
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. ",
keywords = "74-d694, Flo genes, Long reads, Structural variant, Yeast genome, Laboratories, Saccharomyces cerevisiae/genetics, Sequence Analysis, DNA, DNA Transposable Elements, Protein Serine-Threonine Kinases, Saccharomyces cerevisiae Proteins, High-Throughput Nucleotide Sequencing, Chromosomes, long reads, HSP104, MULTIPLE SEQUENCE ALIGNMENT, SACCHAROMYCES-CEREVISIAE, PREDICTION, 74-D694, MUTANTS, FLO genes, DNA, structural variant, PCR",
author = "Barbitoff, {Yury A.} and Matveenko, {Andrew G.} and Matiiv, {Anton B.} and Maksiutenko, {Evgeniia M.} and Moskalenko, {Svetlana E.} and Drozdova, {Polina B.} and Polev, {Dmitrii E.} and Beliavskaia, {Alexandra Y.} and Danilov, {Lavrentii G.} and Predeus, {Alexander V.} and Zhouravleva, {Galina A.}",
note = "Publisher Copyright: {\textcopyright} The Author(s) 2021.",
year = "2021",
month = apr,
doi = "10.1093/g3journal/jkab029",
language = "English",
volume = "11",
journal = "G3: Genes, Genomes, Genetics",
issn = "2160-1836",
publisher = "Genetics Society of America",
number = "4",

}

RIS

TY - JOUR

T1 - Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage

AU - Barbitoff, Yury A.

AU - Matveenko, Andrew G.

AU - Matiiv, Anton B.

AU - Maksiutenko, Evgeniia M.

AU - Moskalenko, Svetlana E.

AU - Drozdova, Polina B.

AU - Polev, Dmitrii E.

AU - Beliavskaia, Alexandra Y.

AU - Danilov, Lavrentii G.

AU - Predeus, Alexander V.

AU - Zhouravleva, Galina A.

N1 - Publisher Copyright: © The Author(s) 2021.

PY - 2021/4

Y1 - 2021/4

N2 - 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.

AB - 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.

KW - 74-d694

KW - Flo genes

KW - Long reads

KW - Structural variant

KW - Yeast genome

KW - Laboratories

KW - Saccharomyces cerevisiae/genetics

KW - Sequence Analysis, DNA

KW - DNA Transposable Elements

KW - Protein Serine-Threonine Kinases

KW - Saccharomyces cerevisiae Proteins

KW - High-Throughput Nucleotide Sequencing

KW - Chromosomes

KW - long reads

KW - HSP104

KW - MULTIPLE SEQUENCE ALIGNMENT

KW - SACCHAROMYCES-CEREVISIAE

KW - PREDICTION

KW - 74-D694

KW - MUTANTS

KW - FLO genes

KW - DNA

KW - structural variant

KW - PCR

UR - http://www.scopus.com/inward/record.url?scp=85104899488&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/4c291dcd-257f-3ed3-a3ad-f0478f6cbd26/

U2 - 10.1093/g3journal/jkab029

DO - 10.1093/g3journal/jkab029

M3 - Article

C2 - 33677552

AN - SCOPUS:85104899488

VL - 11

JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

SN - 2160-1836

IS - 4

M1 - jkab029

ER -

ID: 84957906