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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
..., including DNA- or RNA-mediated duplication and de novo origination, lead to a high rate of protein-coding gene gain in human evolution (Zhang et al. 2012; Zhang and Long 2014). Transcriptome profiling has revealed that new genes in the human postdating the human and mouse split (i.e., primate-specific genes...
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Research: A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
- Tina T. Hu,
- Michael B. Eisen,
- Kevin R. Thornton,
- and Peter Andolfatto
Genome Res. January 2013 23: 89-98; Published in Advance August 30, 2012, doi:10.1101/gr.141689.112
...noncoding DNA sites and significantly slower for synonymous sites. The absence of a X/A difference for putatively neutral sites and the robustness of the pattern to Gene Ontology and sex-biased expression suggest that partly recessive beneficial mutations may comprise a substantial fraction of noncoding DNA...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...like orangutans (Haaf and Schmid 1987; Ijdo et al. 1991; Ventura et al. 2011), such structures are not unique to African great apes. A similar, albeit larger, subterminal heterochromatic cap structure composed of alpha-satellite DNA was described for siamang s from the gibbon lineage (Koga et al. 2012...
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LETTER: Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes
- Anne-Sophie Van Laere,
- Wouter Coppieters,
- and Michel Georges
Genome Res. December 2008 18: 1884-1895; Published in Advance November 3, 2008, doi:10.1101/gr.082487.108
...). Enhanced recombination is also thought to account for the accelerated rate of evolution noted for genes in the PAR (particularly in rodents and to a lesser extent in primates), as recombination is accompanied by DNA repair relying on low-fidelity DNA polymerases ( Perry and Ashworth 1999 ; Filatov...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...the presence of full-length PRDM9 genes in the s of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low...
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Research: Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development
- Kenji Ichiyanagi,
- Yungfeng Li,
- Toshiaki Watanabe,
- Tomoko Ichiyanagi,
- Kei Fukuda,
- Junko Kitayama,
- Yasuhiro Yamamoto,
- Satomi Kuramochi-Miyagawa,
- Toru Nakano,
- Yukihiro Yabuta,
- Yoshiyuki Seki,
- Mitinori Saitou,
- and Hiroyuki Sasaki
Genome Res. December 2011 21: 2058-2066; Published in Advance October 31, 2011, doi:10.1101/gr.123679.111
...Cycle Ruby stain (Invitrogen) and 10% FBS, the cells were sorted on the basis of their fluorescence emission intensity, whichwas correlated with the DNA content, to collect pachytene spermatocytes (4n) and round spermatids (1n). We confirmed high purity (>90%) for the pachytene spermatocyte preparation...
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LETTER: Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
- David A. Ray,
- Cedric Feschotte,
- Heidi J.T. Pagan,
- Jeremy D. Smith,
- Ellen J. Pritham,
- Peter Arensburger,
- Peter W. Atkinson,
- and Nancy L. Craig
Genome Res. May 2008 18: 717-728; Published in Advance March 13, 2008, doi:10.1101/gr.071886.107
...). Supporting this idea, a detailed investigation of the evolutionary history of human DNA transposons revealed that many transposons were intensively active during early primate evolution (∼80–40 million years ago [Mya]), but this activity ceased approximately ∼40 Mya ( Pace and Feschotte 2007 ). Analyses...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...% of all TEs in the human but only ∼10% in zebrafish (International Human Genome Sequencing Consortium 2001; Howe et al. 2013). In contrast, ∼40% of the zebrafish comprises DNA transposons, whereas in humans, they occupy just ∼3% (Pace and Feschotte 2007). Overall, all the major lineages of eukaryotic...
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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: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
...Pol III transcription as opposed to the bystander RNAs from Pol II transcription of the host genes.RAMPAGE is a 5′-complete cDNA sequencing assay that captures the transcription start site (TSS) at single-nucleotide resolution and provides transcript connectivity via paired-end sequencing (Batut et al...

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