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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
.... For brain development, primate-specific KRAB zinc-finger proteins (KZNFs) are specifically up-regulated in the mid-fetal stage, which may have contributed to the evolution of this critical stage. Altogether, hundreds of PSGs are either recruited to processes under strong selection pressure or to processes...
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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
...KRAB, SSXRD, SET, and zinc-finger domains (Fig. 4B). There is no complete homolog of PRDM9 in the M. bellicosus annotation. We therefore used BLAST to search for sequences homologous to the conserved functional domains from C. secundus. We identified a putative PRDM9 ortholog on Scaffold 42 of the M...
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LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
- Aileen M. Smith,
- Maria-Jose Sanchez,
- George A. Follows,
- Sarah Kinston,
- Ian J. Donaldson,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
...appears to reside in distal regulatory elements. However, very little is known about a possible role for transposable elements in the evolution of distal regulatory elements, a situation most likely explained by the relative ease of identifying promoters compared to distal regulatory elements. Despite...
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LETTER: An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
- Leo Goodstadt,
- Andreas Heger,
- Caleb Webber,
- and Chris P. Ponting
Genome Res. July 2007 17: 969-981; Published in Advance May 10, 2007, doi:10.1101/gr.6093907
...similarity to retroviral and transposable elements such as LINE1; and also some noncoding sequence erroneously predicted from the reverse strand of presumably functional protein coding sequence. This resulted in a final protein coding gene count of 18,639. By comparison, our similarly estimated minimum gene...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity...
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Method: Increased taxon sampling reveals thousands of hidden orthologs in flatworms
- José M. Martín-Durán,
- Joseph F. Ryan,
- Bruno C. Vellutini,
- Kevin Pang,
- and Andreas Hejnol
Genome Res. July 2017 27: 1263-1272; Published in Advance April 11, 2017, doi:10.1101/gr.216226.116
...Finder: solving fundamental biases in whole comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16: 157. Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397–405. FitchWM. 1970. Distinguishing homologous from analogous proteins. Syst Zool...
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ARTICLE: Poised for Contagion: Evolutionary Origins of the Infectious Abilities of Invertebrate Retroviruses
- Harmit S. Malik,
- Steve Henikoff,
- and Thomas H. Eickbush
Genome Res. September 1, 2000 10: 1307-1318; doi:10.1101/gr.145000
...these retrotransposable element lineages. Many vertebrate retroviruses have incorporated host genes during their evolution: for example, src in the avian Rous sarcoma virus ( Takeya et al. 1981 ). Thus, one possibility is that the env gene could have been acquired from a host , usurping the normal receptor...
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PERSPECTIVE: Raising the estimate of functional human sequences
- Michael Pheasant and
- John S. Mattick
Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
...) Evolution and multilevel optimization of the genetic code . Genome Res. 17 : 401 – 404 . ↵ Brandt, J. , Schrauth, S. , Veith, A.M. , Froschauer, A. , Haneke, T. , Schultheis, C. , Gessler, M. , Leimeister, C. , Volff, J.N. ( 2005a ) Transposable elements as a source of genetic innovation: Expression...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...that H3K27 methylation plays a role for restricting CTCF binding in early embryos, ensuring proper organization during development.CCCTC-binding factor (CTCF) is a conserved transcriptional regulator composed of 11 central zinc-finger domains (ZFs). It plays a crucial role in 3D organization...
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ARTICLE: Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila
- Mariano Labrador and
- Victor G. Corces
Genome Res. October 2003 13: 2220-2228; doi:10.1101/gr.1440703
...the highest rate of chromosomal evolution reported so far, with an estimated number of sequence disruptions per Mb per million years of only 0.066 to 0.05 ( Ranz et al. 2001 ). We have tested the possibility that transposable elements could be involved in the generation of these rearrangements and concluded...

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