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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
...-quality assemblies can be created from xenic protist cultures by combining deep long-read sequencing with metagenomic assembly techniques, enabling rigorous comparative genomic analyses.ResultsCapturing Blastocystis diversityTo investigate the evolution of the Blastocystis genus, from its initial divergence through...
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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
...of genic region instead of whole size. (CV) conventional bees; (GF) germ-free bees. Gut microbiome and RNA editing Genome Research 3 www..org activity rather than being a consequence of altered host gene expression. Moreover, because the removal of RNA editing will trigger autoimmune response (Liddicoat et...
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Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
- Keyi Geng,
- Lara G. Merino,
- Linda Wedemann,
- Aniek Martens,
- Małgorzata Sobota,
- Yerma P. Sanchez,
- Jonas Nørskov Søndergaard,
- Robert J. White,
- and Claudia Kutter
Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
..., hinting at another unexpected genomic aberration (Fig. 6F).In summary, on-target genomic aberrations can occur frequently at different genomic locations and in different cell lines, irrespective of the delivery methods of the CRISPR-Cas9 system used.DiscussionWe revealed the co-occurrence of multiple...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
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Method: Efficient taxa identification using a pangenome index
- Omar Ahmed,
- Massimiliano Rossi,
- Christina Boucher,
- and Ben Langmead
Genome Res. July 2023 33: 1069-1077; Published in Advance May 31, 2023, doi:10.1101/gr.277642.123
...prokaryotic s reveals clear species boundaries. Nat Commun 9: 5114. doi:10.1038/s41467-018-07641-9 ↵Kim D, Song L, Breitwieser FP, Salzberg SL. 2016. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 26: 1721–1729. doi:10.1101/gr.210641.116 ↵Kovaka S, Fan Y, Ni B, Timp W...
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Resource: Global compositional and functional states of the human gut microbiome in health and disease
- Sunjae Lee,
- Theo Portlock,
- Emmanuelle Le Chatelier,
- Fernando Garcia-Guevara,
- Frederick Clasen,
- Florian Plaza Oñate,
- Nicolas Pons,
- Neelu Begum,
- Azadeh Harzandi,
- Ceri Proffitt,
- Dorines Rosario,
- Stefania Vaga,
- Junseok Park,
- Kalle von Feilitzen,
- Fredric Johansson,
- Cheng Zhang,
- Lindsey A. Edwards,
- Vincent Lombard,
- Franck Gauthier,
- Claire J. Steves,
- David Gomez-Cabrero,
- Bernard Henrissat,
- Doheon Lee,
- Lars Engstrand,
- Debbie L. Shawcross,
- Gordon Proctor,
- Mathieu Almeida,
- Jens Nielsen,
- Adil Mardinoglu,
- David L. Moyes,
- Stanislav Dusko Ehrlich,
- Mathias Uhlen,
- and Saeed Shoaie
Genome Res. June 2024 34: 967-978; Published in Advance July 22, 2024, doi:10.1101/gr.278637.123
...Ehrlich4,17, Mathias Uhlen3 and Saeed Shoaie1,3 1Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom; 2School of Life Sciences, Gwangju Institute of Science and Technology (GIST), 61005, Gwangju, Republic of Korea; 3...
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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
...and strongly associated with the eukaryotic hosts. Thus, their ecology is very different from environmental bacteria, and the extent to which our findings generalize to other environments is currently unclear. Future studies that leverage the ever-increasing global metagenomic sequences will be useful...
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Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...of eukaryotes. We thus developed a specialized deep-learning classifier built upon diverse protozoal, fungal, and prokaryotic s to improve the classification of eukaryotic microbes in the rumen and gut. Leveraging thousands of prokaryotic, fungal, and protozoal s, we developed GutEuk, an ensembled deep...
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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
.../subspecies to investigate how TEs interact with genes associated with host shift. Our results reveal enrichment of TEs at promoter regions of host shift–related genes, with ∼39% of the odorant receptors containing their transcription factor binding sites within TEs. We observe that ∼50% of these TEs are Helitrons...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...and 2D models in capturing the full complexity of higher-order structural influences, we propose a novel three-dimensional (3D) approach. This 3D analysis leverages a deep-learning variational autoencoder-Gaussian mixture model (VAE-GMM) to examine the high-dimensional structural similarities of k...

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