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LETTER: Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
- Scott William Roy and
- David Penny
Genome Res. October 2006 16: 1270-1275; Published in Advance September 8, 2006, doi:10.1101/gr.5410606
.... ↵ Fedorov, A. , Merican, A.F. , Gilbert, W. ( 2002 ) Large-scale comparison of intron positions among animal, plant, and fungal genes . Proc. Natl. Acad. Sci. 99 : 16128 – 16133 . ↵ Fedorov, A. , Roy, S. , Fedorova, L. , Gilbert, W. ( 2003 ) Mystery of intron gain . Genome Res. 13 : 2236 – 2241 . ↵ Ferreira...
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LETTER: Three distinct modes of intron dynamics in the evolution of eukaryotes
- Liran Carmel,
- Yuri I. Wolf,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. July 2007 17: 1034-1044; Published in Advance May 10, 2007, doi:10.1101/gr.6438607
.../kilobase, a greater intron density than in most of the extant fungi and in some animals. The rates of intron gain and intron loss appear to have been dropping during the last ∼1.3 billion years, with the decline in the gain rate being much steeper. Eukaryotic lineages exhibit three distinct modes of evolution...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
..., exploits TEs’ requirement to be expressed in the germline by co-opting them to serve as regulatory elements to gain reproductive fitness. Thus, as TEs coevolved with the host , the germline arose as the prominent site to maximize mutual fitness (Zamudio and Bourc'his 2010; Elbarbary et al. 2016; Zhou et al...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...mapped to the thylacine whole- (WG) assembly, annotated protein-coding (PC) genes (N = 19,356) and noncoding (NC) RNA genes (N = 3613). (B) Exonic enrichment and intronic depletion of RNA reads mapped to exonic and intronic regions of PC genes (at least 10% coverage) in skeletal muscle (N = 236) and skin...
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Method: A new framework for exploratory network mediator analysis in omics data
- Qingpo Cai,
- Yinghao Fu,
- Cheng Lyu,
- Zihe Wang,
- Shun Rao,
- Jessica A. Alvarez,
- Yun Bai,
- Jian Kang,
- and Tianwei Yu
Genome Res. April 2024 34: 642-654; Published in Advance May 7, 2024, doi:10.1101/gr.278684.123
...1 (Park et al. 2005), with major STAT3 response elements located within exon1 and intron1 regions of the AKT1 gene, indicating that AKT1 is a direct target gene of STAT3. Therefore, gaining a better understanding of the regulation of cellular metabolism in breast cancer, particularly the role...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...a habitat generalist, and this forest species has also adapted well to urban areas in some parts of its range while essentially vanishing from others (Meinig and Büchner 2012; Büchner et al. 2024), making its decline an ongoing mystery.Population genetic analysis has been identified as a major research need...
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Research: Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species
- Chris Eberlein,
- Omar Abou Saada,
- Anne Friedrich,
- Warren Albertin,
- and Joseph Schacherer
Genome Res. December 2021 31: 2316-2326; Published in Advance November 23, 2021, doi:10.1101/gr.275380.121
...of the trajectories leading to polyploid s within the same species.Polyploidy, a state in which organisms carry three or more full sets of chromosomes, is a phenomenon that can be observed throughout plant, animal, and fungi species. Polyploidization has gained interest because of its tremendous effects...
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Resource: The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting
- Lishi Li,
- Yulong Song,
- Xinrui Shi,
- Jianheng Liu,
- Shaolei Xiong,
- Wanying Chen,
- Qiang Fu,
- Zichao Huang,
- Nannan Gu,
- and Rui Zhang
Genome Res. January 2018 28: 132-143; Published in Advance December 12, 2017, doi:10.1101/gr.224386.117
...types in human. However, high-level editing is mostly found in neuronal tissues in mouse and Drosophila. Interestingly, the edited miRNAs in neuronal and non-neuronal tissues in human gain two distinct sets of new targets, which are significantly associated with cognitive and organ developmental...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
..., and that many Iroquois –CRMs were ancestrally located within Sowah introns. Retroposition, gene, and genome duplication have allowed selective elimination of Sowah exons from the Iroquois regulatory landscape while keeping associated CRMs, resulting in large associated gene deserts. These results...
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PERSPECTIVE: Genomics of the fungal kingdom: Insights into eukaryotic biology
- James E. Galagan,
- Matthew R. Henn,
- Li-Jun Ma,
- Christina A. Cuomo,
- and Bruce Birren
Genome Res. December 2005 15: 1620-1631; doi:10.1101/gr.3767105
...as an outgroup), and a probabilistic model was used to estimate the most likely rate of intron gain and loss giving rise to these observed conservation patterns. One immediate conclusion stemming from this work was the clear importance of intron gain within this group of Euascomycetes. All three non...

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