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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
..., Spain; 3Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain Corresponding author: jaime.iranzo@cab.inta-csic.esAbstractProkaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGEs...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
.... This study highlights the importance of recombination for phage survival and the diversity of strategies to achieve it.Viruses encode many functions essential for their growth, but host functions are also critical for nearly all viruses. Examples of the latter are functions for energy production (ATP...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...surround the use of auxiliary elements, especially given the lack of any known ones in G. lamblia.To shed light on these fundamental evolutionary questions, we set out to characterize the diversity and evolutionary dynamics of strategies used to recognize poly(A) sites in six protists, including four...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...of transposable elements (TEs), hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defense, we introduced the P-element, one of the most widely studied...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...Evaluation of strategies for evidence-driven annotation using long-read RNA-seq Alejandro Paniagua1,2,6, Cristina Agustín-García1,6, Francisco J. Pardo-Palacios1, Thomas Brown3,4, Maite De Maria5, Nancy D. Denslow5, Camila J. Mazzoni3,4 and Ana Conesa1 1Institute for Integrative Systems Biology...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
..., particularly how to select study subjects, how to determine the number of cells to sequence per subject, and the needed sequencing depth per cell. We also discuss computational strategies for the analysis of single-cell data and describe how single-cell data can be integrated with bulk tissue data and data...
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Research: Cellular abundance shapes function in piRNA-guided genome defense
- Pavol Genzor,
- Parthena Konstantinidou,
- Daniel Stoyko,
- Amirhossein Manzourolajdad,
- Celine Marlin Andrews,
- Alexandra R. Elchert,
- Constantinos Stathopoulos,
- and Astrid D. Haase
Genome Res. November 2021 31: 2058-2068; Published in Advance October 19, 2021, doi:10.1101/gr.275478.121
...Cellular abundance shapes function in piRNA-guided defense Pavol Genzor1,4, Parthena Konstantinidou1,2,4, Daniel Stoyko1,4, Amirhossein Manzourolajdad3, Celine Marlin Andrews1, Alexandra R. Elchert1, Constantinos Stathopoulos2 and Astrid D. Haase1 1National Institute of Diabetes and Digestive...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth Christina A. Cuomo 1 , 5 , 6 , Christopher A. Desjardins 1 , 5 , Malina A. Bakowski 2 , 5 , Jonathan Goldberg 1 , Amy T. Ma 2...
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ARTICLE: Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
- Hidehiro Toh,
- Brian L. Weiss,
- Sarah A.H. Perkin,
- Atsushi Yamashita,
- Kenshiro Oshima,
- Masahira Hattori,
- and Serap Aksoy
Genome Res. February 2006 16: 149-156; Published in Advance December 19, 2005, doi:10.1101/gr.4106106
...Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host Hidehiro Toh 1 , 2 , Brian L. Weiss 3 , Sarah A.H. Perkin 3 , Atsushi Yamashita 1 , Kenshiro Oshima 1...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...preference and the corresponding metabolic strategies that differentiate feeding habits remain elusive. Here, by comparing the whole of a typical carnivorous fish (Leiocassis longirostris Günther) with that of herbivorous fish, we identify 250 genes through both positive selection and rapid evolution...
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