Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Salazar, A.N. (TU Delft Pattern Recognition and Bioinformatics)
Gorter de Vries, A.R. (TU Delft BT/Industriele Microbiologie)
van den Broek, M.A. (TU Delft BT/Industriele Microbiologie)
Brouwers, N. (TU Delft BT/Industriele Microbiologie)
de la Torre, P. (TU Delft BT/Industriele Microbiologie)
Kuijpers, N.G.A. (TU Delft BT/Biotechnologie)
Daran, J.G. (TU Delft BT/Industriele Microbiologie)
Abeel, T.E.P.M.F. (TU Delft Pattern Recognition and Bioinformatics; Broad Institute of MIT and Harvard)

BT/Biotechnologie

2019

Background: The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history. Results: To fill this gap, we generated a chromosome-level genome assembly of the S. pastorianus strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of S. pastorianus strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the S. cerevisiae subgenomes of Group 1 and 2 strains, and marked differences from sequenced S. cerevisiae strains. Conclusions: Our findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous S. cerevisiae strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.

Genome assembly
Lager yeast
Long-read sequencing
Nanopore sequencing

http://resolver.tudelft.nl/uuid:87d4da33-fe2e-43ce-bc8a-ba08ee512b45

https://doi.org/10.1186/s12864-019-6263-3

1471-2164

BMC Genomics, 20 (1), 1-18

Institutional Repository

journal article

© 2019 A.N. Salazar, A.R. Gorter de Vries, M.A. van den Broek, N. Brouwers, P. de la Torre, N.G.A. Kuijpers, J.G. Daran, T.E.P.M.F. Abeel