Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

TY - JOUR

T1 - Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

AU - Etherington, Graham J.

AU - Wu, Pei Shang

AU - Oliferenko, Snezhana

AU - Uhlmann, Frank

AU - Nieduszynski, Conrad A.

N1 - Publisher Copyright: © 2024 The Authors. Yeast published by John Wiley & Sons Ltd.

PY - 2024/3/11

Y1 - 2024/3/11

N2 - Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as “fission yeasts.” As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available 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 the S. japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, 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 of S. japonicus to 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 growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.

AB - Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as “fission yeasts.” As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available 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 the S. japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, 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 of S. japonicus to 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 growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.

KW - centromere

KW - fission yeast

KW - rDNA

KW - Schizosaccharomyces japonicus

KW - telomere

KW - tRNA

UR - https://www.scopus.com/pages/publications/85180892429

U2 - 10.1002/yea.3912

DO - 10.1002/yea.3912

M3 - Article

C2 - 38451028

AN - SCOPUS:85180892429

SN - 0749-503X

VL - 41

SP - 73

EP - 86

JO - Yeast

JF - Yeast

IS - 3

ER -