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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
..., specifically, how adaptive evolution and divergence precipitate HI and ultimately establish reproductive barriers, remains largely unknown. Despite decades of research into the genetic basis of speciation, only a very limited number of genes responsible for HI have been cloned (Maheshwari and Barbash 2011...
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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
...). The piRNA pathway presents features of an adaptive defense system against TE invasion (Aravin et al. 2007; Brennecke et al. 2008; Khurana et al. 2011; Yu et al. 2019), but little is known about the processes driving its evolution. Many piRNA pathway genes encoding the proteins involved in TE silencing...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...sexual recombination, and indicates that aneuploidy is a relevant process in Leishmania’s survival and evolution. Chromosomal duplications were also shown to directly impact gene expression, in which chromosomes with extra copies were highly expressed compared with disomic counterparts, with the sole...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...in contrast to the 178 NLRs that are known in Arabidopsis and 387 in Brachypodium (Michael et al. 2017). In the wa7733 and wa8730 s, we found only a single canonical NLR gene. Although it has conserved homologs in the Spirodela s, it is very divergent from NLR genes of other species. Additionally, two NLR...
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LETTER: Origins and impact of constraints in evolution of gene families
- Boris E. Shakhnovich and
- Eugene V. Koonin
Genome Res. December 2006 16: 1529-1536; Published in Advance October 19, 2006, doi:10.1101/gr.5346206
...correlations have taught us little about evolutionary dynamics governing gene duplication and divergence. Gene duplication followed by divergence is one of the primary driving forces behind functional innovation during evolution ( Ohno 1970 ; Lynch and Katju 2004 ). Currently, the divergence of two paralogs...
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Research: Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen
- Ronnie de Jonge,
- Melvin D. Bolton,
- Anja Kombrink,
- Grardy C.M. van den Berg,
- Koste A. Yadeta,
- and Bart P.H.J. Thomma
Genome Res. August 2013 23: 1271-1282; Published in Advance May 16, 2013, doi:10.1101/gr.152660.112
...environmental conditions. The lack of sexual reproduction, and consequently meiotic recombination, is thought to greatly affect the potential to generate novel genetic combinations. Especially, pathogenic microbes involved in an intimate interaction with a host need to continuously adapt their effector gene...
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Perspective: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
- Lesley T. MacNeil and
- Albertha J.M. Walhout
Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109
...to representing physical interactions, GRN edges can also represent regulatory relationships that can, for instance, be inferred by correlating gene expression profiles between genes and potential regulators. Initially this approach was developed for the yeast Saccharomyces cerevisiae (Segal et al. 2003). More...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...occupancy by key TFs during hematopoietic differentiation, correlate this dynamic binding with changes in gene expression, and search for determinants of differential occupancy. Here we focused on TAL1 (previously known as SCL), a TF that is indispensable atmultiple stages of hematopoiesis. This basic...
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Research: Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species
- Dan Xie,
- Chieh-Chun Chen,
- Leon M. Ptaszek,
- Shu Xiao,
- Xiaoyi Cao,
- Fang Fang,
- Huck H. Ng,
- Harris A. Lewin,
- Chad Cowan,
- and Sheng Zhong
Genome Res. June 2010 20: 804-815; Published in Advance March 10, 2010, doi:10.1101/gr.100594.109
..., the active state of a GRNmodule is drawn. The nodes represent the genes with detectable transcripts; the edges represent the predicted interactions of the connecting nodes. Interactions were predicted by the MATISSE program, using correlation of expression changes in a window of three time points centered...
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LETTER: Computing prokaryotic gene ubiquity: Rescuing the core from extinction
- Robert L. Charlebois and
- W. Ford Doolittle
Genome Res. December 2004 14: 2469-2477; doi:10.1101/gr.3024704
.... ↵ Kunin, V. and Ouzounis, C.A. 2003 . The balance of driving forces during evolution in prokaryotes. Genome Res. 13 : 1589 -1594. ↵ Krylov, D.M., Wolf, Y.I., Rogozin, I.B., and Koonin, E.V. 2003 . Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity...

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