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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
....fischer@sorbonne-universite.fr, zhou.xu@sorbonne-universite.frAbstractTelomeres gradually shorten at each cell division, and telomerase counteracts this shortening by elongating telomere sequences. This dynamic balance between elongation and shortening results in a steady-state telomere length (TL) distribution. Here, we develop...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...-induced cell death, many managed to survive telomerase absence and must have therefore found a solution to maintain and protect telomeres. In this work, using long-read Oxford Nanopore Technologies (“Nanopore”) sequencing able to traverse large repeated regions, we investigated instability in telomerase...
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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...technologies, it is now possible to assemble through human centromeres (Nurk et al. 2022). More recent methods, including NTRprism (Altemose et al. 2022), HORmon (Kunyavskaya et al. 2022), and HiCAT (Gao et al. 2023), can identify detailed chromosome-specific HOR patterns from complete SatDNA sequences...
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Perspective: The genetics and epigenetics of satellite centromeres
- Paul B. Talbert and
- Steven Henikoff
Genome Res. April 2022 32: 608-615; Published in Advance March 31, 2022, doi:10.1101/gr.275351.121
...Bio) SMRT technology and Oxford Nanopore Technologies have cast illumination on previously dark matter, allowing assembly of previously intractable arrays. Whereas short sequencing reads have defined the point centromeres of budding yeast (Fitzgerald-Hayes et al. 1982) and short regional centromeres...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...of centromere tandem repeat arrays has been limited in many species, as they could not be fully assembled using short-read sequencing (Miga and Sullivan 2021). However, Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio) HiFi long-read sequencing now allow complete assembly of complex centromere...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...region begins with chromosome-specific sequences followed by a conserved ribosomal RNA cluster that is followed by the duplicated subtelomeric region and telomere. There are many ONT and PacBio reads that link the unique chromosomal regions and the beginning of the subtelomeric gene families but only...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...Nanopore Technologies (ONT) platform now can routinely generate sequencing reads in excess of 100 kbp (so-called ultralong [UL] sequencing reads) (Nurk et al. 2020; Shafin et al. 2020; Logsdon et al. 2021). The use of parent–child trio (trio-hifiasm) Illumina whole- sequencing (WGS) data in conjunction...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
.../86) overlap complete protein-coding sequence, and 15% (13/86) overlap one or more full-length D. melanogaster genes. In total, 32 complete coding sequences were duplicated, or 12.8 new genes per million years. Similar to the polymorphic duplicates in D. simulans (Rogers et al. 2014), tandem duplications fixed...
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