Article
Multidisciplinary Sciences
G. Ozan Bozdag, Seyed Alireza Zamani-Dahaj, Thomas C. Day, Penelope C. Kahn, Anthony J. Burnetti, Dung T. Lac, Kai Tong, Peter L. Conlin, Aishwarya H. Balwani, Eva L. Dyer, Peter J. Yunker, William C. Ratcliff
Summary: This study investigates the evolution of multicellular organisms using a long-term experiment with snowflake yeast as the model system. The results show that snowflake yeast evolved to be macroscopic in anaerobic conditions, while remaining microscopic in aerobic conditions. This research provides insights into how simple groups of cells overcome biophysical limitations through gradual multicellular evolution.
Article
Cell Biology
Nikolaos Vakirlis, Zoe Vance, Kate M. Duggan, Aoife McLysaght
Summary: This article investigates the origins and conservation of functional microproteins encoded by small open reading frames (sORFs). By tracing the formation and activation of each ORF, it is discovered that novel microproteins with significant phenotypic effects have emerged de novo throughout animal evolution, including two after the human-chimpanzee split.
Article
Multidisciplinary Sciences
William R. Blevins, Jorge Ruiz-Orera, Xavier Messeguer, Bernat Blasco-Moreno, Jose Luis Villanueva-Canas, Lorena Espinar, Juana Diez, Lucas B. Carey, M. Mar Alba
Summary: Recent research has identified 213 de novo originated transcripts in Saccharomyces cerevisiae, with half of them expressed from regions that already contain other genes. These transcripts show similar expression changes in response to stress and some are capable of translating small proteins.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Fides Zenk, Yinxiu Zhan, Pavel Kos, Eva Loeser, Nazerke Atinbayeva, Melanie Schaechtle, Guido Tiana, Luca Giorgetti, Nicola Iovino
Summary: HP1a plays a crucial role in de novo 3D genome organization during Drosophila early development, contributing to clustering and folding of chromosome regions, particularly in the B-compartment.
Review
Ecology
Luuk A. Broeils, Jorge Ruiz-Orera, Berend Snel, Norbert Hubner, Sebastiaan van Heesch
Summary: This review discusses the challenges and controversies surrounding the detection, mechanisms of origin, annotation, validation, and characterization of de novo genes and open reading frames (ORFs). It includes a curated list of de novo genes reported for humans and provides a thorough table with proposed disease associations, protein characteristics, and supporting evidence for translation and protein detection. The work aims to support future explorations of de novo genes and ORFs in humans.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Jose Carlos Montanes, Marta Huertas, Xavier Messeguer, M. Mar Alba
Summary: The formation of new genes can occur through gene duplication or de novo formation from noncoding sequences. Both mechanisms show similarities in terms of low sequence constraints in the initial evolutionary stages, high turnover rates at the species level, and comparable persistence rates in deeper branches. Additionally, de novo proteins tend to have an excess of substitutions between charged amino acids, leading to rapid loss of their initial highly basic character.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Claudio Benicio Cardoso-Silva, Alexandre Hild Aono, Melina Cristina Mancini, Danilo Augusto Sforca, Carla Cristina da Silva, Luciana Rossini Pinto, Keith L. Adams, Anete Pereira de Souza
Summary: Orphan genes (OGs), which are protein-coding genes unique to specific groups or species, have unpredictable functions. This study identified and characterized 319 OGs in sugarcane, and investigated their regulation and expression profiles. The results showed that these OGs are involved in stress response and defense mechanisms in sugarcane.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Eugenio Lopez-Cortegano, Rory J. Craig, Jobran Chebib, Eniolaye J. Balogun, Peter D. Keightley
Summary: Genetic variation arises from different types of spontaneous mutations, including single-nucleotide substitutions, indels, and structural changes. Structural mutations (SMs) are important in genome evolution and have roles in evolutionary adaptation, speciation, and genetic diseases like cancer. In this study, long-read sequencing was used to determine the full mutation spectrum in mutation accumulation (MA) lines of Chlamydomonas reinhardtii. The rate and spectrum of SMs were found to vary between strains, with a substantial proportion of mutations being SMs. Different strains also showed variation in the types of SMs, which were associated with the presence of active transposable elements (TEs). This study highlights the significant role of different types of SMs and TEs in evolution.
Article
Evolutionary Biology
Wojciech M. Karlowski, Deepti Varshney, Andrzej Zielezinski
Summary: In this study, we investigated taxonomically restricted genes (TRGs) in diverse and economically important Bacillus bacteria by examining TRG identification parameters and data sources. We found that sequence similarity thresholds, composition, and the size of the reference database significantly affected the identification process. By applying stringent TRG search parameters and incorporating an analysis of noncoding and non-syntenic regions of non-Bacillus genomes, we minimized false-positive TRG predictions and discovered previously missed genes. Furthermore, we identified potential origins of TRGs by identifying homologous noncoding genomic regions in non-Bacillus species and detected sequence changes that could lead to the formation of protein-coding genes within these regions.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Julie M. Cridland, Alex C. Majane, Li Zhao, David J. Begun
Summary: Research on de novo gene discovery in Drosophila has revealed significant differences in gene abundance and expression between different tissues, particularly in the testis and accessory gland. While other properties such as transcript length and chromosomal distribution are more similar, regulatory mechanisms may vary and interact with selection to produce differences in de novo genes expressed in male reproductive tissues.
Article
Evolutionary Biology
Timothy B. Yates, Kai Feng, Jin Zhang, Vasanth Singan, Sara S. Jawdy, Priya Ranjan, Paul E. Abraham, Kerrie Barry, Anna Lipzen, Chongle Pan, Jeremy Schmutz, Jin-Gui Chen, Gerald A. Tuskan, Wellington Muchero
Summary: Orphan genes, unique to Populus trichocarpa, were identified, and evidence of de novo gene evolution was provided through comparison across different species and genomes. By associating orphan genes with expression quantitative trait loci, common biological themes such as stress response and defense were identified. Additionally, a putative cis-element for a de novo gene and the evolution of a putative transcription factor binding site were described using conserved synteny.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Xiao Liang, Lenwood S. Heath
Summary: This study investigates the relationship between paleoclimate and the emergence of de novo primate genes, and reveals that these genes tend to emerge in the recent 13 million years during a cooling temperature period. Moreover, they are more likely to emerge during local warming periods. Additionally, both primate de novo genes and human cancer-associated genes have later origins compared to random human genes.
G3-GENES GENOMES GENETICS
(2023)
Article
Multidisciplinary Sciences
Kota Kambara, Kaien Fujino, Hanako Shimura
Summary: The study developed a de novo assembly pipeline for transcriptome data of the wild orchid Cypripedium in Japan. The pipeline created a more complete and less redundant contig set by combining multiple data sets and integrating assemblies. Trinity and IDBA-Tran assemblers showed good performance in this study. The contig set obtained can be used as a reference for differential gene expression analysis and other downstream analysis in RNA-seq.
Article
Multidisciplinary Sciences
Dolma Michellod, Tanja Bien, Daniel Birgel, Marlene Violette, Manuel Kleiner, Sarah Fearn, Caroline Zeidler, Harald R. Gruber-Vodicka, Nicole Dubilier, Manuel Liebeke
Summary: Using various techniques, such as metabolite imaging and enzyme assays, we have discovered that gutless marine annelids synthesize the plant sterol sitosterol, which is commonly found in plants. This synthesis is facilitated by a noncanonical C-24 sterol methyltransferase, an enzyme that is essential for sitosterol synthesis in plants but not widely known in most animals. Our phylogenetic analyses also indicate that this enzyme is present in representatives of at least five animal phyla, suggesting that the synthesis of plant-like sterols is more common in animals than previously believed.
Article
Ecology
Ni A. A. An, Jie Zhang, Fan Mo, Xuke Luan, Lu Tian, Qing Sunny Shen, Xiangshang Li, Chunqiong Li, Fanqi Zhou, Boya Zhang, Mingjun Ji, Jianhuan Qi, Wei-Zhen Zhou, Wanqiu Ding, Jia-Yu Chen, Jia Yu, Li Zhang, Shaokun Shu, Baoyang Hu, Chuan-Yun Li
Summary: Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant. The distinctive U1 elements and RNA splice-related sequences drive the origin of de novo genes from lncRNA loci and distinguish them from lncRNAs. The functional new genes acquire functions along with the achievement of their coding potential.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Thomas F. M. Cummings, Kevin Gori, Luis Sanchez-Pulido, Gavriil Gavriilidis, David Moi, Abigail R. Wilson, Elizabeth Murchison, Christophe Dessimoz, Chris P. Ponting, Maria A. Christophorou
Summary: Protein posttranslational modifications add complexity to biological systems. This study reveals the evolutionary trajectory of peptidylarginine deiminases (PADIs) in animals and provides evidence that PADIs were introduced into animals through horizontal gene transfer from cyanobacteria.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Thomas J. Colgan, Andres N. Arce, Richard J. Gill, Ana Ramos Rodrigues, Abdoulie Kanteh, Elizabeth J. Duncan, Li Li, Lars Chittka, Yannick Wurm
Summary: This study analyzed the genomes of Bombus terrestris bumblebees in Great Britain and found genetic diversity within the population as well as signatures of recent adaptation affecting key processes. Unusual genomic features were also discovered, indicating the resilience of this pollinator species to future pressures. Applying this approach to other species can help understand their adaptive potential and develop conservation strategies.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Anindita Brahma, Raphael Gray Leon, Gabriel Luis Hernandez, Yannick Wurm
Summary: Cooperative living benefits animals in dominating ecosystems, but also increases the risk of pathogen exposure. Research on red fire ants shows that queens from multiple-queen colonies have higher viral load and diversity, highlighting a previously overlooked cost of transitioning to more highly social living.
Article
Evolutionary Biology
Cuong Cao Dang, Bui Quang Minh, Hanon McShea, Joanna Masel, Jennifer Eleanor James, Le Sy Vinh, Robert Lanfear
Summary: This study introduces a new maximum likelihood method, nQMaker, that can estimate time nonreversible amino acid substitution models and rooted phylogenetic trees. The results show that the nonreversible models estimated with nQMaker are a better fit to empirical alignments than pre-existing reversible models, and the improvements in model fit scale with the size of the data set.
SYSTEMATIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Alina Nicheperovich, Adrian M. Altenhoff, Christophe Dessimoz, Sina Majidian
Summary: Conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology. The use of traditional model systems such as mice, rats, and zebrafish is costly and time-consuming, and raises ethical concerns. To address these issues, the Orthologous Matrix and Alternative Model Organism (OMAMO) software and web service provides users with the best non-complex organism for research based on orthologous relationships between humans and other species.
Article
Ecology
Thomas Bataillon, Thomas H. G. Ezard, Michael Kopp, Joanna Masel
Article
Evolutionary Biology
Rodrigo Pracana, Richard Burns, Robert L. Hammond, Benjamin C. Haller, Yannick Wurm
Summary: This study uses the SLiM simulation environment to create a new model for simulating genetic evolution in haplodiploid species. The researchers find that selection on recessive mutations is more effective in haplodiploids than in diploids. The open-source model developed in this study enhances our understanding of social evolution and the response of ecologically important haplodiploid species to environmental changes.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Luke J. Kosinski, Nathan R. Aviles, Kevin Gomez, Joanna Masel
Summary: Proteins, as the workhorses of the cell, can cause harm through misfolding and aggregation. However, sometimes proteins can be born from noncoding DNA without harm. By studying the fitness of different Escherichia coli lineages expressing unique random peptides, researchers found that simple amino acid frequencies, rather than the ordering of amino acids, predicted lineage fitness. Smaller amino acids that promote intrinsic structural disorder had less harmful effects on fitness. These amino acids were also enriched in young animal proteins.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Alicja Witwicka, Federico Lopez-Osorio, Valentine Patterson, Yannick Wurm
Summary: Global losses of insects caused by insecticides targeting nicotinic acetylcholine receptors (nAChRs) have neurotoxic effects on beneficial insects. Understanding the use and composition of nAChRs is crucial for evaluating and predicting the effects of such insecticides. Our analysis of gene expression data from honey bees and bumble bees reveals spatial and temporal variations in the expression of nAChR subunits. These findings provide a likely mechanism for the damaging effects of nAChR-targeting insecticides on insects and emphasize the importance of considering molecular target variation in risk assessment.
Article
Biochemistry & Molecular Biology
Jennifer E. James, Paul G. Nelson, Joanna Masel
Summary: Protein domains that emerged recently have higher disorder and clustering of hydrophobic residues. There is a hypothesis that different levels of selection affect the retention probabilities of domains with different properties. Loss rates were inferred for animal Pfam domains and were found to depend on disorder and clustering trait values. The results support the hypothesis that domain loss slowly eliminates domains with suboptimal disorder and clustering levels, affecting proteome composition.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck, Christophe Dessimoz
Summary: Current methods for phylogenetic tree inference are computationally expensive and laborious, with limitations in sequencing coverage, assembly and annotation quality. To address this, Read2Tree directly processes raw sequencing reads into gene groups, bypassing traditional steps in phylogeny inference, and achieves high accuracy. It outperforms assembly-based approaches in terms of speed and accuracy across various datasets, including a yeast tree of life and classification of Coronaviridae samples. Read2Tree enables comparative genomics at scale without genome assembly or annotation.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ana Lopez Vazquez, Laure Allenbach Petrolati, Martina Legris, Christophe Dessimoz, Edwin R. Lampugnani, Natasha Glover, Christian Fankhauser
Summary: PHYTOCHROME KINASE SUBSTRATE (PKS) proteins are involved in light-modulated changes in growth orientation, controlling hypocotyl gravitropism in the light and acting early in phototropin signaling. PKS sequences are restricted to seed plants and share 6 motifs. Motif C is S-acylated on conserved cysteines, mediating the association of PKS proteins with the plasma membrane.
Editorial Material
Multidisciplinary Sciences
David Moi, Christophe Dessimoz
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Public, Environmental & Occupational Health
Joanna Masel, James Ian Mackie Petrie, Jason Bay, Wolfgang Ebbers, Aalekh Sharan, Scott Michael Leibrand, Andreas Gebhard, Samuel Zimmerman
Summary: Digital contact tracing and notification have not lived up to expectations in combating the COVID-19 pandemic due to multiple points of failure. Research indicates that achieving a significant reduction in transmission risk requires high success rates in technology adoption, contact detection, prompt diagnosis and notification, and behavior change. Recommendations include emphasizing user autonomy, integrating tracing/notification apps with testing, manual contact tracing, and scientific data collection.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2023)
Article
Biochemistry & Molecular Biology
Adrian M. Altenhoff, Alex Warwick Vesztrocy, Charles Bernard, Clement-Marie Train, Alina Nicheperovich, Silvia Prieto Banos, Irene Julca, David Moi, Yannis Nevers, Sina Majidian, Christophe Dessimoz, Natasha M. Glover
Summary: In this update paper, the authors present the latest developments in the OMA browser knowledgebase, including new species additions, exploration of ancestral genomes, and new tools in the OMA Ecosystem. These developments provide exciting opportunities for orthology analysis and comparative genomics.
NUCLEIC ACIDS RESEARCH
(2023)