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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
..., indicates sites under purifying selection (ω2a) or neutral evolution (ω2b) in the outgroups but under positive selection in the Tortricidae.We asked whether phylogenetic clades with the SA fusion (Tortricidae) had different rates of molecular evolution from those without SA fusion. Within a phylogenetic...
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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
...of a single, ancestrally fused chromosome into four distinct ones. We also detect other bryozoan-specific fusions: ALGs A1 and C2 initially fused (A1 ⊗ C2) and then divided into two chromosomes (e.g., M. membranacea Chr 6 and Chr 8); ALG P joined with the lophotrochozoan fusion K ⊗ O2 (P ⊗ K ⊗ O2) and later...
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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
...site, including a 250-bp flank on each end and including the insertion sequence, if the haplotype contained the SV allele, and we matched both SNV alleles (including the 8-bp flank) to each extracted haplotype region.We then counted the number of occurrences for each SNV allele in haplotypes...
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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: The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
- Drew R. Schield,
- Daren C. Card,
- Nicole R. Hales,
- Blair W. Perry,
- Giulia M. Pasquesi,
- Heath Blackmon,
- Richard H. Adams,
- Andrew B. Corbin,
- Cara F. Smith,
- Balan Ramesh,
- Jeffery P. Demuth,
- Esther Betrán,
- Marc Tollis,
- Jesse M. Meik,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. April 2019 29: 590-601; Published in Advance March 21, 2019, doi:10.1101/gr.240952.118
...-specific expression) lacked NFI binding sites and were, on average, further (86 kb) away from the nearest GRHL1 binding site; binding sites for either set of TFs were not, however, statistically enriched in venom gene regions compared to the genomic background (Supplemental Table S13; Supplemental Methods). The up...
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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
...; Supplemental Table S1), except Lachancea fantastica that has only seven chromosomes because of a telomere-to-telomere fusion (Supplemental Fig. S2; Supplemental Table S2). The genomic GC content ranges from 41.2%– 47.3% (Supplemental Table S2). In L. kluyveri, a region of 1Mb containing the MAT locus...
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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
...duplications. Nature 437: 88–93. The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee and comparison with the human . Nature 437: 69–87. Fan Y, Linardopoulou E, Friedman C, Williams E, Trask BJ. 2002. Genomic structure and evolution of the ancestral chromosome fusion site...
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Research: An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
- Djivan Prentout,
- Olga Razumova,
- Bénédicte Rhoné,
- Hélène Badouin,
- Hélène Henri,
- Cong Feng,
- Jos Käfer,
- Gennady Karlov,
- and Gabriel A.B. Marais
Genome Res. February 2020 30: 164-172; Published in Advance February 7, 2020, doi:10.1101/gr.251207.119
...-studied heteromorphic systems in plants are characterized by a Y Chromosome larger than the X due to fast accumulation of repeats on the former, as in Silene latifolia or Coccinia grandis (Matsunaga et al. 1994; Sousa et al. 2013, 2016; Hobza et al. 2017), or multiple Y Chromosomes due to chromosomal fission–fusion...
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Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
..., 2013. Accepted June 13, 2013. © 2013, Published by Cold Spring Harbor Laboratory Press This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site...

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