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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
.... First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole...
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Research: Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes
- Huiquan Liu,
- Qinhu Wang,
- Yi He,
- Lingfeng Chen,
- Chaofeng Hao,
- Cong Jiang,
- Yang Li,
- Yafeng Dai,
- Zhensheng Kang,
- and Jin-Rong Xu
Genome Res. April 2016 26: 499-509; Published in Advance March 2, 2016, doi:10.1101/gr.199877.115
...Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes Huiquan Liu 1 , Qinhu Wang 1 , Yi He 2 , Lingfeng Chen 1 , Chaofeng Hao 1 , Cong Jiang 1 , Yang Li 3 , Yafeng Dai 1 , Zhensheng Kang 1...
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Method: Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes
- Lena Tasse,
- Juliette Bercovici,
- Sandra Pizzut-Serin,
- Patrick Robe,
- Julien Tap,
- Christophe Klopp,
- Brandi L. Cantarel,
- Pedro M. Coutinho,
- Bernard Henrissat,
- Marion Leclerc,
- Joël Doré,
- Pierre Monsan,
- Magali Remaud-Simeon,
- and Gabrielle Potocki-Veronese
Genome Res. November 2010 20: 1605-1612; Published in Advance September 14, 2010, doi:10.1101/gr.108332.110
...of the human distal gut microbiome. Science 312: 1355–1359. Meta screening to boost enzyme discovery Genome Research 1611 www..org Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perriere G, Simonet P, et al. 2004. Phylogenetic analysis of polyketide synthase I domains from...
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Resource: Genome-scale phylogenetic function annotation of large and diverse protein families
- Barbara E. Engelhardt,
- Michael I. Jordan,
- John R. Srouji,
- and Steven E. Brenner
Genome Res. November 2011 21: 1969-1980; Published in Advance July 22, 2011, doi:10.1101/gr.104687.109
...Genome-scale phylogenetic function annotation of large and diverse protein families Barbara E. Engelhardt 1 , 4 , 6 , Michael I. Jordan 1 , 2 , John R. Srouji 3 , 5 and Steven E. Brenner 3 1Electrical Engineering and Computer...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...; Miyauchi et al. 2020) have demonstrated that high TE content and a reduced set of plant cell wall–degrading enzymes are recurring genomic features among ECM fungi. As all known Tuberaceae species exhibit an ECM lifestyle (Bonito and Smith 2016), this family represents a valuable model for investigating...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...and Greider 2003). TL must therefore maintain a minimal length to allow for cell division. In most species, including budding yeast, this is accomplished by expressing the telomerase enzyme, which preferentially adds telomeric repeats to shorter telomeres (Greider and Blackburn 1985; Lundblad and Szostak 1989...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...adenocarcinomas, including some metabolic enzymes with the potential to be neofunctional. The postduplication diversification of driver genes and functions may indicate selection for somatic copy number changes in lung tumors and an increased scope for tumor adaptations.Cancers result from the evolutionary...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...al. 2024). Limited phylogenetic analyses of SET domain proteins across 20 representative fungal species suggested extensive gene duplications, losses, and domain rearrangements, implying unique HMT regulatory mechanisms in fungi (Ding et al. 2022). However, comprehensive, systematic analysis of SET...
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LETTER: Phylogenetic Footprint Analysis of IGF2 in Extant Mammals
- Jennifer R. Weidman,
- Susan K. Murphy,
- Catherine M. Nolan,
- Fred S. Dietrich,
- and Randy L. Jirtle
Genome Res. September 2004 14: 1726-1732; doi:10.1101/gr.2774804
...Phylogenetic Footprint Analysis of IGF2 in Extant Mammals Jennifer R. Weidman 1 , Susan K. Murphy 2 , Catherine M. Nolan 4 , Fred S. Dietrich 3 , and Randy L. Jirtle 1 , 5 1 Department of Radiation Oncology, Duke...

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