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

Graham J. Etherington; Pei Shang Wu; Snezhana Oliferenko; Frank Uhlmann; Conrad A. Nieduszynski

doi:10.1002/yea.3912

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

Graham J. Etherington^*, Pei Shang Wu, Snezhana Oliferenko, Frank Uhlmann, Conrad A. Nieduszynski^*

^*Corresponding author for this work

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

2 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	73-86
Number of pages	14
Journal	Yeast
Volume	41
Issue number	3
DOIs	https://doi.org/10.1002/yea.3912
Publication status	Published - Mar 2024

Keywords

centromere
fission yeast
rDNA
Schizosaccharomyces japonicus
telomere
tRNA

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title = "Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features",

abstract = "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.",

keywords = "centromere, fission yeast, rDNA, Schizosaccharomyces japonicus, telomere, tRNA",

author = "Etherington, {Graham J.} and Wu, {Pei Shang} and Snezhana Oliferenko and Frank Uhlmann and Nieduszynski, {Conrad A.}",

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AU - Etherington, Graham J.

AU - Wu, Pei Shang

AU - Oliferenko, Snezhana

AU - Uhlmann, Frank

AU - Nieduszynski, Conrad A.

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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.

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

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Keywords

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