Cory Gardner, Junhao Chen, Christina Hadfield, Zhaolian Lu, David Debruin, Yu Zhan, Maureen Donlin, Tae-Hyuk Ahn, Zhenguo Lin
{"title":"Chromosome-level subgenome-aware de novo assembly of Saccharomyces bayanus provides insight into genome divergence after hybridization","authors":"Cory Gardner, Junhao Chen, Christina Hadfield, Zhaolian Lu, David Debruin, Yu Zhan, Maureen Donlin, Tae-Hyuk Ahn, Zhenguo Lin","doi":"10.1101/gr.279364.124","DOIUrl":null,"url":null,"abstract":"Interspecies hybridization is prevalent in various eukaryotic lineages and plays important roles in phenotypic diversification, adaptation, and speciation. To better understand the changes that occurred in the different subgenomes of a hybrid species and how they facilitate adaptation, we completed chromosome-level de novo assemblies of all chromosomes for a recently formed hybrid yeast, <em>Saccharomyces bayanus</em> strain CBS380, using Nanopore MinION long-read sequencing. We characterized the <em>S. bayanus</em> genome and compared it with its parent species, <em>S. uvarum</em> and <em>S. eubayanus</em>, and other <em>S. bayanus</em> genomes to better understand genome evolution after a relatively recent hybridization event. We observed multiple recombination events between the subgenomes in each chromosome, followed by loss of heterozygosity (LOH) in nine chromosome pairs. In addition to maintaining nearly all gene content and synteny from its parental genomes, <em>S. bayanus</em> has acquired many genes from other yeast species, primarily through the introgression of <em>S. cerevisiae</em>, such as those involved in the maltose metabolism. Finally, the patterns of recombination and LOH suggest an allotetraploid origin of <em>S. bayanus</em>. The gene acquisition and rapid LOH in the hybrid genome probably facilitated its adaptation to maltose brewing environments and mitigated the maladaptive effect of hybridization. This manuscript describes the first in-depth study using long-read sequencing technology of an <em>S. bayanus</em> hybrid genome which may serve as an excellent reference for future studies of this important yeast and other yeast strains.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":null,"pages":null},"PeriodicalIF":6.2000,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1101/gr.279364.124","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Interspecies hybridization is prevalent in various eukaryotic lineages and plays important roles in phenotypic diversification, adaptation, and speciation. To better understand the changes that occurred in the different subgenomes of a hybrid species and how they facilitate adaptation, we completed chromosome-level de novo assemblies of all chromosomes for a recently formed hybrid yeast, Saccharomyces bayanus strain CBS380, using Nanopore MinION long-read sequencing. We characterized the S. bayanus genome and compared it with its parent species, S. uvarum and S. eubayanus, and other S. bayanus genomes to better understand genome evolution after a relatively recent hybridization event. We observed multiple recombination events between the subgenomes in each chromosome, followed by loss of heterozygosity (LOH) in nine chromosome pairs. In addition to maintaining nearly all gene content and synteny from its parental genomes, S. bayanus has acquired many genes from other yeast species, primarily through the introgression of S. cerevisiae, such as those involved in the maltose metabolism. Finally, the patterns of recombination and LOH suggest an allotetraploid origin of S. bayanus. The gene acquisition and rapid LOH in the hybrid genome probably facilitated its adaptation to maltose brewing environments and mitigated the maladaptive effect of hybridization. This manuscript describes the first in-depth study using long-read sequencing technology of an S. bayanus hybrid genome which may serve as an excellent reference for future studies of this important yeast and other yeast strains.
期刊介绍:
Launched in 1995, Genome Research is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine.
Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies.
New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are presented electronically on the journal''s web site where appropriate. The journal also provides Reviews, Perspectives, and Insight/Outlook articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.