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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...in MA lines derived from two strains (CC-1952 and CC-2931) of the green alga Chlamydomonas reinhardtii. The SM rate is highly variable between strains and between MA lines, and SMs represent a substantial proportion of all mutations in both strains (CC-1952 6%; CC-2931 12%). The SM spectra differ...
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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
...Telomeric repeat evolution in the phylum Nematoda revealed by high-quality assemblies and subtelomere structures Jiseon Lim1,2, Wonjoo Kim1,2, Jun Kim1,3,4 and Junho Lee1,2,3 1Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea; 2Institute of Molecular...
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Resource: Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
...assembly to the level of pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb). We identified structural variations that affected as many as 2694 genes, most of which are at chromosome arms. Subtelomeric regions contained the most extensive genomic rearrangements, which even created new...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...Rearrangements of viral and human s at human papillomavirus integration events and their allele-specific impacts on cancer regulation Vanessa L. Porter1,2,3, Michelle Ng1,3, Kieran O'Neill1, Signe MacLennan1,2,3, Richard D. Corbett1, Luka Culibrk1,4, Zeid Hamadeh5,6, Marissa Iden7,8, Rachel Schmidt...
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Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
- Jesper Eisfeldt,
- Adam Ameur,
- Felix Lenner,
- Esmee Ten Berk de Boer,
- Marlene Ek,
- Josephine Wincent,
- Raquel Vaz,
- Jesper Ottosson,
- Tord Jonson,
- Sofie Ivarsson,
- Sofia Thunström,
- Alexandra Topa,
- Simon Stenberg,
- Anna Rohlin,
- Anna Sandestig,
- Margareta Nordling,
- Pia Palmebäck,
- Magnus Burstedt,
- Frida Nordin,
- Eva-Lena Stattin,
- Maria Sobol,
- Panagiotis Baliakas,
- Marie-Louise Bondeson,
- Ida Höijer,
- Kristine Bilgrav Saether,
- Lovisa Lovmar,
- Hans Ehrencrona,
- Malin Melin,
- Lars Feuk,
- and Anna Lindstrand
Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
...: anna.lindstrand@ki.se; lars.feuk@igp.uu.seAbstractClinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes and small deletions...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...Plant evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence Scott Ferguson1,4, Ashley Jones1,4, Kevin Murray1,2, Rose Andrew3, Benjamin Schwessinger1 and Justin Borevitz1 1Research School of Biology, Australian National University, Canberra...
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Research: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements
- Luisa Berná,
- Pablo Marquez,
- Andrés Cabrera,
- Gonzalo Greif,
- María E. Francia,
- and Carlos Robello
Genome Res. May 2021 31: 823-833; Published in Advance April 27, 2021, doi:10.1101/gr.262832.120
...Reevaluation of the Toxoplasma gondii and Neospora caninum s reveals misassembly, karyotype differences, and chromosomal rearrangements Luisa Berná1, Pablo Marquez1, Andrés Cabrera1, Gonzalo Greif1, María E. Francia2,3 and Carlos Robello1,4 1Laboratory of Host Pathogen Interactions...
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Research: Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
- Rob W. Ness,
- Andrew D. Morgan,
- Radhakrishnan B. Vasanthakrishnan,
- Nick Colegrave,
- and Peter D. Keightley
Genome Res. November 2015 25: 1739-1749; Published in Advance August 10, 2015, doi:10.1101/gr.191494.115
...Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii Rob W. Ness 1 , Andrew D. Morgan 1 , Radhakrishnan B. Vasanthakrishnan 1 , Nick Colegrave 1 , 2 and Peter D. Keightley 1 , 2...
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Research: Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs
- Adrian A. Valli,
- Bruno A.C.M. Santos,
- Silvia Hnatova,
- Andrew R. Bassett,
- Attila Molnar,
- Betty Y. Chung,
- and David C. Baulcombe
Genome Res. April 2016 26: 519-529; Published in Advance March 11, 2016, doi:10.1101/gr.199703.115
...Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs Adrian A. Valli 1 , Bruno A.C.M. Santos 1 , Silvia Hnatova 1 , Andrew R. Bassett 1 , 2...
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Resource: Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
- Tatiana Maroilley,
- Stephane Flibotte,
- Francesca Jean,
- Victoria Rodrigues Alves Barbosa,
- Andrew Galbraith,
- Afiya Razia Chida,
- Filip Cotra,
- Xiao Li,
- Larisa Oncea,
- Mark Edgley,
- Don Moerman,
- and Maja Tarailo-Graovac
Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122
...rearrangements. Their structures have been mostly explored with low-resolution genetic techniques (e.g., fluorescence in situ hybridization or PCR), before genomic mapping and molecular characterization through sequencing became feasible. As a result, the precise nature of most chromosomal rearrangements remains...

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