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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...Poecilia wingei and Poecilia obscura (Nanda et al. 2014). This analysis revealed polymorphisms in heterochromatin content of the Y as well as differences in distance of the genetic marker M_229 to the physical chromosome end between populations. The sex determination locus (SDL) was mapped to the most...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...architecture necessary for superloop formation. Species with rearranged X Chromosomes retain the ancestral order and relative spacing of loci critical for superloop formation during XCI, with compensatory inversions evolving to maintain these long-range physical interactions.The X Chromosome is the most well...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...Chromosome-scale assemblies of Acanthamoeba castellanii s provide insights into Legionella pneumophila infection–related chromatin reorganization Cyril Matthey-Doret1,2,6, Morgan J. Colp3,6, Pedro Escoll4, Agnès Thierry1, Pierrick Moreau1, Bruce Curtis3, Tobias Sahr4, Matt Sarrasin5, Michael W...
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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
..., independently of its interaction with Rap1, and Sir4 and Sir2 activity, or chromosome context (Fig. 6C). This strongly suggests that Sir3–Sir3 interactions provide the physical link that holds together Sir3-bound loci.View larger version: In this window In a new window Figure 6. Arrays of Sir3 are sufficient...
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Research: Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming
- Adrian Janiszewski,
- Irene Talon,
- Joel Chappell,
- Samuel Collombet,
- Juan Song,
- Natalie De Geest,
- San Kit To,
- Greet Bervoets,
- Oskar Marin-Bejar,
- Caterina Provenzano,
- Lotte Vanheer,
- Jean-Christophe Marine,
- Florian Rambow,
- and Vincent Pasque
Genome Res. October 2019 29: 1659-1672; Published in Advance September 12, 2019, doi:10.1101/gr.249706.119
...Leuven, 3000 Leuven, Belgium ↵5 These authors contributed equally to this work. Corresponding author: vincent.pasque@kuleuven.beAbstractInduction and reversal of chromatin silencing is critical for successful development, tissue homeostasis, and the derivation of induced pluripotent stem cells (iPSCs). X-Chromosome...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
...concentrate in distal regions (Saintenac et al. 2009; Choulet et al. 2014). For example, 82% of crossovers on Chromosome 3B occur within 19% of its physical length (Darrier et al. 2017). Bread wheat is an allohexaploid, comprising homoeologous A, B, and D subs of seven chromosomes each (2n = 6x = 42, AABBDD...
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Resource: A chromosome-scale assembly of the axolotl genome
- Jeramiah J. Smith,
- Nataliya Timoshevskaya,
- Vladimir A. Timoshevskiy,
- Melissa C. Keinath,
- Drew Hardy,
- and S. Randal Voss
Genome Res. February 2019 29: 317-324; Published in Advance January 24, 2019, doi:10.1101/gr.241901.118
...into 14 chromosomes. Moreover, we used fluorescence in situ hybridization to verify the structure of these 14 scaffolds and assign each to its corresponding physical chromosome. This new assembly covers 27.3 Gb and encompasses 94% of annotated gene models on chromosomal scaffolds. We show the assembly...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...in Table 2. The assembled M. caroli chromosomes do not exhibit any large inter-chromosomal rearrangements with respect to the M. musculus , which was expected from physical maps as well as chromosome paintings (Thybert et al. 2018). However, we detected a large cluster of inversions in Chromosome 17 of ∼5...
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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
...the true level of synteny across these species.View larger version: In this window In a new window Figure 1. Syntenic relationships between select Cryptosporidium chromosome assemblies. (A) Synteny between Chromosomes 2, 4, and 5. Vertical black lines within a chromosome represent known physical gaps...
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Research: The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner
- Richard P. Meisel,
- Christopher A. Gonzales,
- and Hoang Luu
Genome Res. August 2017 27: 1417-1426; Published in Advance June 15, 2017, doi:10.1101/gr.215509.116
...Richard P. Meisel,1 Christopher A. Gonzales,1,2 and Hoang Luu1 1Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA Canonical ancient sex chromosome pairs consist of a gene rich X (or Z) Chromosome and a male-limited (or female-limited) Y (or W) Chromosome...

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