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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...by duplication at the pericentromeric region of ancestral Chromosome 10. Evolutionary genomic rearrangements, assembly gaps in ape references, and interlocus gene conversion hamper the identification of ancestral Chromosome 10 copies, 1:1 orthology relationships between ape s, and lineage-specific more recent...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...repetitive nature (Nurk et al. 2022). These advances have transformed our understanding of architecture, showing how segmental duplications contribute to evolutionary innovation and genomic diversity, while also illuminating the structural organization of centromeres and their role in chromosome segregation...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
..., Santa Cruz, California 95064, USA; 3UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; 4Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Corresponding authors: jcahill@rockefeller.edu, ejarvis@rockefeller.eduAbstractVocal learning, the ability...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
..., genomic, and gene content comparisons of three honey bee species. (Left to right) Maximum likelihood phylogeny built from 9310 concatenated single-copy orthologous proteins from sequenced honeybees and bumblebee outgroup indicated that A. florea diverged first from the most recent common ancestor of honey...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
.... For example, the 2009 identification of the mutation that causes SCA31 was achieved solely by “traditional” methods: bacterial artificial chromosome (BAC)-based cloning, Sanger sequencing, and Southern blot, with targeted shotgun resequencing (Sato et al. 2009).The techniques employed by the Human Genome...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
..., USA Corresponding author: dcpage@wi.mit.eduAbstractLittle is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across...
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Method: A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission
- Mikhail Liskovykh,
- Nikolay V. Goncharov,
- Nikolai Petrov,
- Vasilisa Aksenova,
- Gianluca Pegoraro,
- Laurent L. Ozbun,
- William C. Reinhold,
- Sudhir Varma,
- Mary Dasso,
- Vadim Kumeiko,
- Hiroshi Masumoto,
- William C. Earnshaw,
- Vladimir Larionov,
- and Natalay Kouprina
Genome Res. October 2019 29: 1719-1732; Published in Advance September 12, 2019, doi:10.1101/gr.254276.119
...completing the annotation of genetic loci controlling chromosome transmission.Genome-wide siRNA screens have been used to interrogate a variety of molecular mechanisms related to increased sensitivity to ionizing radiation or spontaneous gamma H2AX (phosphorylated histone H2AX at serine 139) (Paulsen et al...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...of sequence classes derived from several independent autosomal transposition events, as well as retention and expansion of ancestral X–Y orthologs (Fig. 1A–C). We identified three separate autosomal transpositions that occurred at different periods in the evolutionary history of the felid Y Chromosome. We...
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Resource: The genomic architecture and molecular evolution of ant odorant receptors
- Sean K. McKenzie and
- Daniel J.C. Kronauer
Genome Res. November 2018 28: 1757-1765; Published in Advance September 24, 2018, doi:10.1101/gr.237123.118
...sequencing (Pacific Biosciences [PacBio] and Oxford Nanopore) and Hi-C proximity-based scaffolding to assemble a high-quality, chromosome-level for the clonal raider ant. We used this assembly to study the genomic organization and genomic context of chemosensory genes in the clonal raider ant and compared...
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Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116
....3, displayed in light green) and 16 (16p13.1–13.3, displayed in light blue). Macaque signals on Chromosome 20 are homologous to human Chromosome 16p13.3. Mohajeri et al. 1458 Genome Research www..org Figure 4. Orangutan sequence assembly of REPD and REPP orthologous regions. (A) A 1.56-Mbp region...

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