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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
.... Nonetheless, bacteria offer several unique avenues for research into the process and mechanics of gene birth at a resolution not feasible in other organisms. Both their amenability to experimental evolutionary analysis and their strain-level variation in gene content foster investigations of how noncoding...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...that their patterns of molecular evolution may differ from those of unicellular and traditional multicellular algae.As for life cycle types, we anticipate haploid lineages to experience more purifying selection owing to the haploid life stage being prone to elimination of deleterious mutations (Orr and Otto 1994...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...by a poly-adenylation (poly[A]) track, such that oligos that enhance transcription from the promoter can be identified by sequencing of the resulting noncoding RNAs (Fig. 1A). A total of 34,344 bi-allelic variants were selected to test for allele-specific enhancer activity in our STARR-seq library. Alleles...
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Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
- Kejia Wen,
- Lijuan Yang,
- Tuanlin Xiong,
- Chao Di,
- Danhui Ma,
- Menghua Wu,
- Zhaoyu Xue,
- Xuedi Zhang,
- Li Long,
- Weimin Zhang,
- Jiaying Zhang,
- Xiaolin Bi,
- Junbiao Dai,
- Qiangfeng Zhang,
- Zhi John Lu,
- and Guanjun Gao
Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
...Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China Long noncoding RNAs (lncRNAs), a recently discovered class of cellular RNAs, play important roles in the regulation of many cellular developmental processes. Although lncRNAs have been systematically identified...
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Research: Less effective selection leads to larger genomes
- Tristan Lefébure,
- Claire Morvan,
- Florian Malard,
- Clémentine François,
- Lara Konecny-Dupré,
- Laurent Guéguen,
- Michèle Weiss-Gayet,
- Andaine Seguin-Orlando,
- Luca Ermini,
- Clio Der Sarkissian,
- N. Pierre Charrier,
- David Eme,
- Florian Mermillod-Blondin,
- Laurent Duret,
- Cristina Vieira,
- Ludovic Orlando,
- and Christophe Jean Douady
Genome Res. June 2017 27: 1016-1028; Published in Advance April 19, 2017, doi:10.1101/gr.212589.116
...N/dS variation across sites andmakes it possible to differentiate between variation in the intensity of purifying (w−) and positive selection (w+) and their respective frequencies. Subterranean species do not show an elevated frequency [ fq(w+)] or intensity of positive selection (w+) but show higher w− (Table 1...
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Research: RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system
- Dan Bar-Yaacov,
- Ernest Mordret,
- Ruth Towers,
- Tammy Biniashvili,
- Clara Soyris,
- Schraga Schwartz,
- Orna Dahan,
- and Yitzhak Pilpel
Genome Res. October 2017 27: 1696-1703; Published in Advance September 1, 2017, doi:10.1101/gr.222760.117
...Tyr to Cys at position 29 of hokB enhances its toxicity. Discussion Why do bacteria exercise RNA editing? In mammalian cells, editing occurs mostly in noncoding regions (Bazak et al. 2014). In bacteria, however, as we have shown, out of the 15 novel A-to-I sites, 12 occurwithin knownprotein...
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Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
- Eyal Elyashiv,
- Kevin Bullaughey,
- Shmuel Sattath,
- Yosef Rinott,
- Molly Przeworski,
- and Guy Sella
Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
...of Jerusalem, Jerusalem 91905, Israel; 4 Department of Human Genetics, University of Chicago, Chicago 60637, USA; 5 Howard Hughes Medical Institute, University of Chicago, Chicago 60637, USA Abstract How much does the intensity of purifying selection vary among populations...
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LETTER: A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
- Kousuke Hanada,
- Xu Zhang,
- Justin O. Borevitz,
- Wen-Hsiung Li,
- and Shin-Han Shiu
Genome Res. May 2007 17: 632-640; Published in Advance March 29, 2007, doi:10.1101/gr.5836207
...or partial genome sequences. In 3997 coding sORFs with readily identifiable homologous sequences, 2376 are subject to purifying selection at the 1% false-positive rate. After eliminating coding sORFs with similarity to known transposable elements and those that are likely missing exons of known genes...
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Research: Young proteins experience more variable selection pressures than old proteins
- Anchal Vishnoi,
- Sergey Kryazhimskiy,
- Georgii A. Bazykin,
- Sridhar Hannenhalli,
- and Joshua B. Plotkin
Genome Res. November 2010 20: 1574-1581; Published in Advance October 4, 2010, doi:10.1101/gr.109595.110
...Abstract It is well known that young proteins tend to experience weaker purifying selection and evolve more quickly than old proteins. Here, we show that, in addition, young proteins tend to experience more variable selection pressures over time than old proteins. We demonstrate this pattern in three...
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LETTER: Widespread balancing selection and pathogen-driven selection at blood group antigen genes
- Matteo Fumagalli,
- Rachele Cagliani,
- Uberto Pozzoli,
- Stefania Riva,
- Giacomo P. Comi,
- Giorgia Menozzi,
- Nereo Bresolin,
- and Manuela Sironi
Genome Res. February 2009 19: 199-212; Published in Advance November 7, 2008, doi:10.1101/gr.082768.108
...of the expected per site heterozygosity, and π ( Nei and Li 1979 ), the average number of pairwise sequence nucleotide differences. Positive values of D T indicate an excess of intermediate frequency variants and are a hallmark of balancing selection; negative D T-values indicate either purifying selection...

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