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.

Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast

“…accuracy of this estimate is further supported by our estimate of the S. octosporus-S. osmophilus split, which was within 0.3 MY of the previously calculated split (Jia et al, 2023). CBS5679 also contains a repeat-rich gene-sparse region on contig 13, homologous to chromosome 2 in S. japonicus, suggesting that the formation of this feature, which shows close similarity to the centromere of chromosome 2 (Etherington et al, 2023) occurred before the two diverged.…”

“…Additionally, the availability of telomere-to-telomere assemblies (e.g. Etherington et al, 2023) will provide further clarity of centromeric, telomeric, and repeat structure.…”

Nanopore sequencing reveals that DNA replication compartmentalisation dictates genome stability and instability inTrypanosoma brucei

“…Here, we decided to ask if Oxford Nanopore Technologies sequencing might complement Müller et al’s PacBio and Hi-C assembly of the T. brucei Lister 427 genome 9 and help us resolve unanswered questions about DNA replication dynamics. The utility of long-read Nanopore sequencing for genome assembly has recently been demonstrated in T. cruzi , where the presence of many multigene families and abundant transposable elements proved to be a considerable impediment to assembly 22,23 , while it has also allowed telomere-to-telomere chromosome assemblies of several other genomes 24,25 . One notable feature of Nanopore sequencing is the generation of ultra-long (hundreds of kb) reads, which we reasoned in T. brucei may allow increased understanding of repetitive regions in the genome, amongst which the very long centromeres 9,26,27 , estimated to be 20-120 kb in size 28 , are very early-acting origins 14 .…”