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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...separate chromosomes. ALG γ was maintained alone on one chromosome (Chr 7), but genes from this ALG also dispersed to all other chromosomes (Fig. 4D). The C. mucedo exhibits a structure more derived from the ancestral state, characterized by numerous fission and fusion events with limited mixing, resulting...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite's speciation, named collectively as the trypanosomatid ancestral supernumerary chromosome (TASC). TASC has most genes in the same coding strand, is expressed as a disomic chromosome (even...
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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
...et al. 2016). Chr 2 is a fusion of Chr 7 with Chr 24 (Fraser et al. 2020) of Xiphophorus, which represents the basal poeciliid karyotype (Cimino 1974). This fusion was also observed in the assembly of Poecilia picta (Metzger et al. 2021).Assembly, genomic organization, and gene content of the Y...
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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...; Schneider et al. 2017) hosts annotations including genes (O'Leary et al. 2016; Frankish et al. 2021), regulatory regions (The ENCODE Project Consortium 2012; The ENCODE Project Consortium et al. 2020), and repeats (Benson 1999; Bailey et al. 2002; Smit 2013–2015), and it has become a universal coordinate...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...sequence, TBC1D3 copies, and USP6—a hominoid fusion gene of TBC1D3—are illustrated in maroon, red, and green, respectively. TBC1D3 demarcates the boundaries of large-scale rearrangements on chromosome phylogenetic group XVII. (B) TBC1D3 duplication block (cluster of colored arrows) demarcates the boundary...
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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
...regions via chromosomal inversions approximated a linear process over time (Bhutkar et al. 2008). At a broader evolutionary scale, reconstructions of ancestral gene content in Proteobacteria and Archaea showed that gene losses and/or duplications correlated with amino acid substitution rates (Snel et al...
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LETTER: Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13–2q14.1 and Paralogous Regions on Other Human Chromosomes
- Yuxin Fan,
- Elena Linardopoulou,
- Cynthia Friedman,
- Eleanor Williams,
- and Barbara J. Trask
Genome Res. November 1, 2002 12: 1651-1662; doi:10.1101/gr.337602
....e., 2qFus-Dist and 2qFus-Prox are the regions forming the distal and proximal sides of the 2q fusion site, respectively; both were at chromosome tips when the duplicative transfers occurred). Ancestral and derived states, when indicated, are inferred from breaks that disrupt genes, specific repetitive...
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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
...genes (other than the ancestral male determiner), or it could have fused to an autosome (Carvalho and Clark 2005; Larracuente et al. 2010). Alternatively, the house fly Y Chromosome could have arisen through the fusion of the ancestral Y and X Chromosomes. However, after an X-Y fusion, the neo-Y should...
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Research: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
- Mario Ventura,
- Claudia R. Catacchio,
- Saba Sajjadian,
- Laura Vives,
- Peter H. Sudmant,
- Tomas Marques-Bonet,
- Tina A. Graves,
- Richard K. Wilson,
- and Evan E. Eichler
Genome Res. June 2012 22: 1036-1049; Published in Advance March 14, 2012, doi:10.1101/gr.136556.111
...-Aldrich Syndrome Protein and SCAR Homolog (WASH) gene family (Linardopoulou et al. 2007). This gene family has both expanded within the subtelomeric regions, with a copy located specifically at the site of the chromosome 2 fusion. The function of the specific family members is not known, but as a class...
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Research: Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes
- Stephen R. Voss,
- D. Kevin Kump,
- Srikrishna Putta,
- Nathan Pauly,
- Anna Reynolds,
- Rema J. Henry,
- Saritha Basa,
- John A. Walker,
- and Jeramiah J. Smith
Genome Res. August 2011 21: 1306-1312; Published in Advance April 11, 2011, doi:10.1101/gr.116491.110
...and after the divergence of salamanders and frogs. Fourth, we use the outgroup perspective provided by Ambystoma and X. tropicalis data to reconstruct the origin of chicken chromosomes by fission, fusion, and retention of ancestral chromosomes. Results Construction of an Ambystoma gene map Single nucleotide...

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