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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...observed in mice (Vara et al. 2021), muntjac deer (Yin et al. 2021), and yeast (Di Stefano et al. 2020). This specific chromosome structuring could be significant, as multiple-level chromatin organization has been shown to influence gene expression, recombination, and mutation in various species (Li et al...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...pathogenic fungi with large regional type centromeres, such as the closely related stem rust fungus Puccinia graminis f. sp. tritici (Sperschneider et al. 2021), a human pathogenic yeast Cryptococcus neoformans (Yadav et al. 2018b), and an ascomycetous phytopathogen Verticillium dahliae (Seidl et al. 2020...
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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
...; Talbert et al. 2002; Allshire and Karpen 2008). In humans and yeast, the kinetochore consists of approximately 30 core subunits, within which CENP-A/Cse4 recruits the constitutive centromere-associated network (CCAN) (Yu et al. 2000; Yan et al. 2019; Pesenti et al. 2022; Yatskevich et al. 2022). CCAN...
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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
..., possibly aiding in adaptation, evolution, and speciation processes. However, as the effects and mechanisms of translocations have been less studied than other rearrangements (Robberecht et al. 2013), it remains to be seen if they are more likely to have functional/adaptive significance.Although new long...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
...M, Liu L, Dickinson Q, Peris D, Wrobel RL, et al. 2018. Natural variation in the multidrug efflux pump SGE1 underlies ionic liquid tolerance in yeast. Genetics 210: 219–234. doi:10.1534/genetics.118.301161 ↵Hou J, Friedrich A, de Montigny J, Schacherer J. 2014. Chromosomal rearrangements as a major...
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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...evidence for this “genomic shock hypothesis” in the fission yeast Schizosaccharomyces pombe. In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data to assemble s of 37 samples derived from 31 S. pombe strains...
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Research: Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species
- Chris Eberlein,
- Omar Abou Saada,
- Anne Friedrich,
- Warren Albertin,
- and Joseph Schacherer
Genome Res. December 2021 31: 2316-2326; Published in Advance November 23, 2021, doi:10.1101/gr.275380.121
...the Brettanomyces bruxellensis yeast species, which is found in anthropized environments (e.g., beer, contaminant of wine, kombucha, and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid s, we phased them by using different strategies and found that each...
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Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
- Mihaela Ola,
- Caoimhe E. O'Brien,
- Aisling Y. Coughlan,
- Qinxi Ma,
- Paul D. Donovan,
- Kenneth H. Wolfe,
- and Geraldine Butler
Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
.... We report here that isolates of the pathogenic yeast species Candida parapsilosis show within-species polymorphism for the location of centromeres on two of its eight chromosomes. Its old centromeres have an inverted-repeat (IR) structure, whereas its new centromeres have no obvious structural...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus Nikolaos Vakirlis 1 , 6 , Véronique Sarilar 2 , 6 , Guénola Drillon 1 , 6 , Aubin Fleiss 1 , Nicolas Agier...
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Research: Small chromosomal regions position themselves autonomously according to their chromatin class
- Harmen J.G. van de Werken,
- Josien C. Haan,
- Yana Feodorova,
- Dominika Bijos,
- An Weuts,
- Koen Theunis,
- Sjoerd J.B. Holwerda,
- Wouter Meuleman,
- Ludo Pagie,
- Katharina Thanisch,
- Parveen Kumar,
- Heinrich Leonhardt,
- Peter Marynen,
- Bas van Steensel,
- Thierry Voet,
- Wouter de Laat,
- Irina Solovei,
- and Boris Joffe
Genome Res. June 2017 27: 922-933; Published in Advance March 24, 2017, doi:10.1101/gr.213751.116
...-desert locus at 96.5 Mb at the NEO-site and contained telomere sequences at its BLAS-end (Fig. 1). Additionally, in both Autonomous properties of small chromosome segments Genome Research 923 www..org HACs, the hHOR region demonstrated multiple rearrangements with concomitant DNA copy number changes...

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