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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian s Anguo Liu1,2,7, Nini Wang1,3,7, Guoxiang Xie1,2,7, Yang Li1,2, Xixi Yan1,2, Xinmei Li1,2, Zhenliang Zhu2,4,5, Zhuohui Li1,2, Jing Yang2,4,5, Fanxin Meng1, Mingle Dou1,2, Weihuang Chen1, Nange...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...to be caused by GC-biased gene conversion (Mugal et al. 2015). In addition, the uniform numbers of recombination per chromosome (Dumont and Payseur 2008) have been thought to explain the chromosome length-dependent GC content variation between different chromosomes. Our observations did not show pronounced...
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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
...to a zygote nucleus: This creates new MICs and MACs, whereas the new developing MAC (anlagen) already transcribes some genes involved in development (Furrer et al. 2017; Rzeszutek et al. 2020).The genomic structures between MICs and MACs are quite different. MICs contain thousands of short transposon remnants...
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Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
...of differential gene expression (n = 9658 autosomal genes) using the number of protein–protein interactions (PPI), tissue specificity (τ), intraspecific variation in gene expression (ϕ), the ratios of nonsynonymous to synonymous diversity (πN/πS) and divergence (dN/dS), and genomic differentiation between the two...
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Method: Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS)
- Daniela Nachmanson,
- Shenyi Lian,
- Elizabeth K. Schmidt,
- Michael J. Hipp,
- Kathryn T. Baker,
- Yuezheng Zhang,
- Maria Tretiakova,
- Kaitlyn Loubet-Senear,
- Brendan F. Kohrn,
- Jesse J. Salk,
- Scott R. Kennedy,
- and Rosa Ana Risques
Genome Res. October 2018 28: 1589-1599; Published in Advance September 19, 2018, doi:10.1101/gr.235291.118
...Targeted fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS) Daniela Nachmanson1, Shenyi Lian1,3, Elizabeth K. Schmidt1, Michael J. Hipp1, Kathryn T. Baker1, Yuezheng Zhang1, Maria Tretiakova1...
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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...are primarily driven by the underlying pattern of mutation, which accounts for 60% of the variance in base composition across the tree of life (Long et al. 2018). In addition, in some taxa, NSPs are also strongly affected by GC-biased gene conversion (gBGC), a process associated to meiotic recombination...
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Research: Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
- William Gao,
- Carlos J. Gallardo-Dodd,
- and Claudia Kutter
Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
...). In contrast, work in mammals has suggested that adaptation to anticodon pools cannot explain the majority of synonymous codon usage, which appear to be more strongly influenced by mutational biases and drift (dos Reis et al. 2004), in particular GC-biased gene conversion (Pouyet et al. 2017). Despite weak...
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Method: A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets
- Sunjin Moon and
- Joshua M. Akey
Genome Res. June 2016 26: 834-843; Published in Advance April 14, 2016, doi:10.1101/gr.203059.115
.... 2015. Quantification of GC-biased gene conversion in the human . Genome Res 25: 1215–1228. ↵Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science 185: 862–864. ↵Gulko B, Hubisz MJ, Gronau I, Siepel A. 2015. A method for calculating probabilities of fitness...
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Method: Extending the spectrum of DNA sequences retrieved from ancient bones and teeth
- Isabelle Glocke and
- Matthias Meyer
Genome Res. July 2017 27: 1230-1237; Published in Advance April 13, 2017, doi:10.1101/gr.219675.116
...Genome Research 1235 www..org to the manufacturer’s instructions using the QX200 ddPCR EvaGreen Supermix (Bio-Rad), primers CL201 and CL202 (200 nM each) (Supplemental Table S5), and 1 µL template. Library preparation, quantification, and amplification DNA libraries were prepared from 1-, 3-, 9-, and 27...

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