Telomere-to-telomereSchizosaccharomyces japonicusgenome assembly reveals hitherto unknown genome features

Abstract

AbstractSchizosaccharomyces japonicusbelongs to the single-genus class Schizosaccharomycetes, otherwise known as ‘fission yeasts’. As part of a composite model system with its widely studiedS. pombesister species,S. japonicushas provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makesS. japonicusa valuable model organism in its own right. However, the currently available short-read genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of theS japonicusgenome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNAs, transfer RNAs, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size ofS. japonicusto at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growingS. japonicusresearch community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.Take-awayA telomere-to-telomere genome assembly of the fission yeastS. japonicusChromosome 2 harbours a previously unknown second centromere-like regionThe estimated genome size ofS. japonicusmay be up to 18.12 Mb