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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...diagnostic yield (Mastrorosa et al. 2023), LRS could provide a clear path forward. Here, we focus on diagnostic applications of haplotype-aware methylation analysis:Imprinting disordersGenomic imprinting refers to the parent-of-origin specific expression of genes; the classic example is the H19/IGF2 locus...
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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
...family Felidae but show high transcript diversity, copy number variation, and structural rearrangement. Our analysis of ampliconic gene evolution unveils a complex pattern of long-term gene content stability despite extensive structural variation on a nonrecombining background.Advances in DNA sequencing...
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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
...that were misinterpreted as lineage-specific acquisition.Here, we sought to address several outstanding questions about mammalian X Chromosome architecture and ampliconic gene family evolution by expanding the phylogenetic sampling of high-quality s in a comparative analysis. First, we wanted to determine...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying evolution and its consequences for phenotypic evolution in these genetic model species.Repetitive DNA sequences comprise a substantial fraction of the s of multicellular eukaryotes, occupying >40% of human...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...in the evolution of domesticated S. cerevisiae strains showing more rapid copy number variation than wild strains (Bergström et al. 2014; Yue et al. 2017; Duan et al. 2018). To investigate the extent to which gene families differed between sister natural lineages, we de novo assembled, annotated, and inferred...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
...Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (mi...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...can alter tissue dynamics and lead to cancer initiation. Although large-scale sequencing projects have illuminated processes that influence somatic mutation and subsequent tumor evolution, the mutational dynamics operating in the very early stages of cancer development are currently not well...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...(TE) from the hAT family played a critical role in the diversification of gsdfY via introduction of transcription factor-binding sites associated with the initiation and regulation of testicular development. This study is the first in the scenario of MSD gene evolution via allelic diversification...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...-seq in conjunction with molecular cytogenetics, we generated a complete map of inversions between human and macaque and identified variants affecting key genes that may be essential in understanding the evolution of specific human traits. Thus, this study represents a critical resource for genomic research...
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Research: One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin
- Alexej Abyzov,
- Livia Tomasini,
- Bo Zhou,
- Nikolaos Vasmatzis,
- Gianfilippo Coppola,
- Mariangela Amenduni,
- Reenal Pattni,
- Michael Wilson,
- Mark Gerstein,
- Sherman Weissman,
- Alexander E. Urban,
- and Flora M. Vaccarino
Genome Res. April 2017 27: 512-523; Published in Advance February 24, 2017, doi:10.1101/gr.215517.116
...discover candidatemosaic variants at the level of the whole but also conduct extensive validation experiments, demonstrating that the majority of discovered candidates represent genuine mosaic variants in the original fibroblast cells. Results Approach For each person in the families included in this study...

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