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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...in triplicate on the same plate, with a negative control using RNase-free water as the template. RACE of Adar gene in honeybee The full-length nucleotide sequence of Adar was amplified using the rapid-amplification of cDNA ends (RACE) technique with the HiScript-TS 5′/3′ RACE kit (Vazyme RA101). Gene...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
..., PanTax (fast) demonstrates comparable overall performance to KMCP on Illumina data sets but substantially outperforms all other methods on long-read data sets.Benchmarking PanTax against long-read meta assemblers for strain-level profilingWith the rapid development of long-read meta assemblers...
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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
...Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology Abigail L. Lind1,2, Nathan A. McDonald2,3, Elias R. Gerrick4, Ami S. Bhatt5,6 and Katherine S. Pollard1,7,8 1Gladstone Institute for Data Science...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed s from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...-specific piCs arose exclusively from maternally inherited piRNAs as piRNAs from such piCs could not be differentiated from the piRNAs produced from insertions in large common piCs (Supplemental Fig. S12).In summary, a picture is emerging in which the rapid evolution of piCs among D. melanogaster strains...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...different preferences. Transposable elements are a source of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Here, we perform genomic and transcriptomic analyses in six s of cactophilic species...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
..., Université de Lyon, Lyon 69007, France; 4Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne 69622, France ↵5 These authors contributed equally to this work. Corresponding authors: domitille.chalopin-fillot@u-bordeaux.fr, sophie...
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Research: Evolution of transcription factor binding through sequence variations and turnover of binding sites
- Gat Krieger,
- Offir Lupo,
- Patricia Wittkopp,
- and Naama Barkai
Genome Res. June 2022 32: 1099-1111; Published in Advance May 26, 2022, doi:10.1101/gr.276715.122
..., we identify cases of binding-site turnover, in which binding sites are reciprocally gained and lost, yet most interspecific differences remained uncompensated. Our results show the flexibility of TFs to bind imprecise motifs and the fast evolution of TF binding sites between related species...
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Research: Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
- Morteza Roodgar,
- Benjamin H. Good,
- Nandita R. Garud,
- Stephen Martis,
- Mohan Avula,
- Wenyu Zhou,
- Samuel M. Lancaster,
- Hayan Lee,
- Afshin Babveyh,
- Sophia Nesamoney,
- Katherine S. Pollard,
- and Michael P. Snyder
Genome Res. August 2021 31: 1433-1446; Published in Advance July 22, 2021, doi:10.1101/gr.265058.120
...they generalize the stronger environmental perturbations associated with antibiotic treatment. These sudden environmental shifts could uncover cryptic phenotypic differences between previously coexisting strains, driving rapid shifts in the frequencies of segregating genetic variants (Paaby and Rockman 2014).High...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...Evolution of -wide methylation profiling technologies Carolina Montano1,2 and Winston Timp1 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA; 2Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia...
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