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Method: Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes
- Dana Sherill-Rofe,
- Dolev Rahat,
- Steven Findlay,
- Anna Mellul,
- Irene Guberman,
- Maya Braun,
- Idit Bloch,
- Alon Lalezari,
- Arash Samiei,
- Ruslan Sadreyev,
- Michal Goldberg,
- Alexandre Orthwein,
- Aviad Zick,
- and Yuval Tabach
Genome Res. March 2019 29: 439-448; Published in Advance February 4, 2019, doi:10.1101/gr.241414.118
...is not yet fully mapped. Phylogenetic profiling analysis, which detects functional linkage between genes using coevolution, is a powerful approach to identify factors in many pathways. Nevertheless, phylogenetic profiling has limited predictive power when analyzing pathways with complex evolutionary dynamics...
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Research: Coevolution within a transcriptional network by compensatory trans and cis mutations
- Dwight Kuo,
- Katherine Licon,
- Sourav Bandyopadhyay,
- Ryan Chuang,
- Colin Luo,
- Justin Catalana,
- Timothy Ravasi,
- Kai Tan,
- and Trey Ideker
Genome Res. December 2010 20: 1672-1678; Published in Advance October 26, 2010, doi:10.1101/gr.111765.110
...Coevolution within a transcriptional network by compensatory trans and cis mutations Dwight Kuo 1 , Katherine Licon 1 , Sourav Bandyopadhyay 1 , Ryan Chuang 1 , Colin Luo 1 , Justin Catalana 1 , Timothy Ravasi 1 , 2...
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Methods: Reconstructing ancestral gene content by coevolution
- Tamir Tuller,
- Hadas Birin,
- Uri Gophna,
- Martin Kupiec,
- and Eytan Ruppin
Genome Res. January 2010 20: 122-132; Published in Advance November 30, 2009, doi:10.1101/gr.096115.109
...). As it is not clear how to model the evolution of a network withmany types of interactions, we decided to use the generalized MP as an objective function. This leads us to the definition of the computational problem we are concerned with, the ancestral coevolution problem: Given a coevolutionary forest (a set...
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Research: Coevolution of retroelements and tandem zinc finger genes
- James H. Thomas and
- Sean Schneider
Genome Res. November 2011 21: 1800-1812; Published in Advance July 22, 2011, doi:10.1101/gr.121749.111
...Coevolution of retroelements and tandem zinc finger genes James H. Thomas 1 and Sean Schneider Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA Abstract Vertebrate genomes encode large and highly variable...
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LETTER: Coevolution of gene families in prokaryotes
- Otto X. Cordero,
- Berend Snel,
- and Paulien Hogeweg
Genome Res. March 2008 18: 462-468; Published in Advance January 29, 2008, doi:10.1101/gr.6815508
...of the coevolution map and tried to understand the observed features from an evolutionary point of view. Networks of coevolving families are built by considering all pairs of families with a minimum coevolutionary score. Figure 1B shows that the coevolution network is a disconnected graph formed by separate clusters...
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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. 2000. Co-evolution of proteins with their interaction partners. J Mol Biol 299: 283–293. doi:10.1006/jmbi.2000.3732 ↵Hammond CM, Strømme CB, Huang H, Patel DJ, Groth A. 2017. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol...
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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
...in meiosis, suggesting that meiotic sex chromosome inactivation (MSCI) may antagonize the coevolution of KZFPs and ERVs in mammals. Our study uncovers a mechanism by which a subset of KZFPs regulate ERVs to sculpt germline transcriptomes. We propose that epigenetic programming during the transition from...
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ARTICLE: The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint
- Cristian I. Castillo-Davis,
- Fyodor A. Kondrashov,
- Daniel L. Hartl,
- and Rob J. Kulathinal
Genome Res. May 2004 14: 802-811; doi:10.1101/gr.2195604
...The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint Cristian I. Castillo-Davis 1 , Fyodor A. Kondrashov 2 , Daniel L. Hartl 1 , and Rob J. Kulathinal 1 , 3 1...
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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
...constitute a principal driver of evolution, shaping its architecture and regulatory networks. In this context, Tuberaceae can become an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we investigate the interplay between TEs and Tuberaceae...
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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
...a possible coevolution of this gene family with TEs. Alternatively, it may also suggest that ORs are located in TE-rich regions of the s. To investigate this hypothesis, we identified TE-rich regions (Supplemental Fig. S5) and analyzed the frequency of ORs. We observed a single OR in TE-rich regions in D...

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