Article
Biology
Victoria C. C. Moris, Lars Podsiadlowski, Sebastian Martin, Jan Philip Oeyen, Alexander Donath, Malte Petersen, Jeanne Wilbrandt, Bernhard Misof, Daniel Liedtke, Markus Thamm, Ricarda Scheiner, Thomas Schmitt, Oliver Niehuis
Summary: This study reveals a group of genes in honey bees that play an important role in the synthesis of cuticular hydrocarbons, and the predicted functions of these genes are consistent with current knowledge of cuticular hydrocarbon metabolism.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O'Geen, Megan Y. Dennis
Summary: Evidence shows that in humans, paralogous segmental duplication genes exhibit different expression patterns, possibly due to relaxed selection or neofunctionalization. While ancestral paralogs show greater expression conservation with chimpanzee orthologs, certain derived paralogs may retain or supplant ancestral functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
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
Biology
Datian Lang, Xiaoping Wang, Chunbing Liu, Weihang Geng, David M. Irwin, Shanyuan Chen, Chunqing Li, Li Yu, Heng Xiao
Summary: This study reveals a complex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla. The duplication of RNase9 genes might have been advantageous for promoting sperm motility and male fertility, which occurred during the middle Eocene. However, all RNase9 genes were lost in the Cetacean lineage, possibly in response to adaptations to a fully aquatic environment and a balance to the demands of ocean resources.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Juan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Melendez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones
Summary: Studying the evolutionary history of gene families is important for understanding gene origin, evolution, and their implications for functional studies. The sirtuin gene family, involved in aging-related functions, has a complex duplicative history, but our results provide a well-resolved phylogeny and shed light on the repertoire of sirtuin genes among vertebrates. We identified a new member (SIRT3.2) that was lost in amniotes but retained in other jawed vertebrates, and its experimental analysis revealed its mitochondrial location and deacetylase activity similar to mammalian SIRT3.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Catherine Damerval, Carmine Claudot, Martine Le Guilloux, Natalia Conde e Silva, Veronique Brunaud, Ludivine Soubigou-Taconnat, Jose Caius, Etienne Delannoy, Sophie Nadot, Florian Jabbour, Yves Deveaux
Summary: TCP transcription factors are important in developmental processes and hormonal pathways. We studied the TCP genes in the plant species Nigella damascena and found that they are orthologs of TCP genes in Aquilegia coerulea. Phylogenetic analysis and amino acid motif identification suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. There have been independent duplications in core eudicots and Ranunculales, resulting in different numbers of paralogs within TCP gene subclasses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Joao Ricchio, Fabiana Uno, A. Bernardo Carvalho
Summary: The evolution of Drosophila Y chromosomes is mainly driven by gene gains, with a pattern of gene duplication from autosomal regions to the Y chromosome observed. Segmental duplications from autosomes to the Y were found, with most duplicated genes becoming pseudogenes or disappearing, except for a few functional copies like GK20609. Chance plays a significant role in the acquisition of new genes by the Drosophila Y chromosome.
Article
Plant Sciences
Yue Zhang, Qian Zhang, Xingyu Yang, Xiaofeng Gu, Jinming Chen, Tao Shi
Summary: This study compared the 6mA methylation patterns of four lotus plants using nanopore sequencing and compared them to patterns in Arabidopsis and rice. The results showed that 6mA sites are enriched around transcriptional start sites and positively correlated with gene expression levels in lotus, Arabidopsis, and rice. Additionally, 6mA methylation is more conserved in whole-genome duplicates than in local duplicates. Overall, this study reveals the potential role of 6mA methylation in gene regulatory evolution in plants.
Article
Multidisciplinary Sciences
Shuji Shigenobu, Yoshinobu Hayashi, Dai Watanabe, Gaku Tokuda, Masaru Y. Hojo, Kouhei Toga, Ryota Saiki, Hajime Yaguchi, Yudai Masuoka, Ryutaro Suzuki, Shogo Suzuki, Moe Kimura, Masatoshi Matsunami, Yasuhiro Sugime, Kohei Oguchi, Teruyuki Niimi, Hiroki Gotoh, Masaru K. Hojo, Satoshi Miyazaki, Atsushi Toyoda, Toru Miura, Kiyoto Maekawa
Summary: Termites are social organisms with a polyphenic caste system, and gene duplication plays a crucial role in their social evolution. The duplicated genes in the termite genome are associated with caste-biased gene expression and diverse social functions, contributing to caste-specialized functions. Gene duplication facilitates social evolution through regulatory diversification, leading to caste-biased expression and subfunctionalization and/or neofunctionalization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Michael DeGiorgio, Raquel Assis
Summary: CLOUD, a multi-layer neural network based on a model of gene expression evolution, classifies duplicate gene retention mechanisms and predicts their evolutionary parameters with high accuracy and power. It outperforms the previous method CDROM, providing accurate parameter predictions and enhancing understanding of the forces driving duplicate gene evolution and long-term retention. The application of CLOUD to empirical data from Drosophila supports previous findings about gene duplication, highlighting the rapid emergence of new functions in younger duplicate gene copies driven by strong natural selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Zhiguo Dang, Min Zhu, Huarui Chen, Ye Zhang, Aiping Gao, Weihong Ma, Yeyuan Chen, Yunxie Wei, He Zhang
Summary: This study identified the important role of MiMYB10 in regulating pigments, particularly in promoting carotenoid accumulation and controlling peel color. The findings provided new options for breeding strategies aiming to improve fruit quality.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Plant Sciences
Linying Du, Zhenbing Ma, Hude Mao
Summary: Gene duplication is a common phenomenon in biology that impacts genomic variation and diversity, particularly in plant evolution and genetic engineering. Duplicated genes contribute to the emergence of novel functionality and adaptability to abiotic stress. Understanding the effects and mechanisms of gene duplication is crucial for future crop research and the development of high-performance, stress-resistant wheat lines.
Article
Plant Sciences
Licao Cui, Hao Cheng, Zhe Yang, Chuan Xia, Lichao Zhang, Xiuying Kong
Summary: Wheat is a staple food crop that provides 20% of total human calorie consumption. Duplicated genes in wheat evolved faster with shorter gene lengths, higher codon usage bias, lower expression levels, and higher tissue specificity. Duplicated genes have important biological functions, particularly in response to environmental stresses, and different duplication modes exhibit asymmetrical evolutionary patterns. This study lays the foundation for future functional studies on wheat.
Article
Biotechnology & Applied Microbiology
Ayda Mirsalehi, Dragomira N. Markova, Mohammadmehdi Eslamieh, Esther Betran
Summary: Duplications of nuclear transport genes in Drosophila are mainly composed of a few classes of genes that are RNA mediated and evolve rapidly. These duplications may reflect the selected features of nuclear transport.
Article
Evolutionary Biology
Zoe Vance, Lukasz Niezabitowski, Laurence D. Hurst, Aoife McLysaght
Summary: Research has shown that duplicated genes evolve at a faster rate compared to singleton genes in multiple lineages. This phenomenon is not restricted to a single lineage and has implications for the interpretation of gene duplication. Additionally, some singleton genes appear to evolve faster due to homology detection failure and unidentified paralogs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
J. D. Gibson, O. Niehuis, B. R. E. Peirson, E. I. Cash, J. Gadau
Article
Biochemistry & Molecular Biology
Daniel F. Simola, Lothar Wissler, Greg Donahue, Robert M. Waterhouse, Martin Helmkampf, Julien Roux, Sanne Nygaard, Karl M. Glastad, Darren E. Hagen, Lumi Viljakainen, Justin T. Reese, Brendan G. Hunt, Dan Graur, Eran Elhaik, Evgenia V. Kriventseva, Jiayu Wen, Brian J. Parker, Elizabeth Cash, Eyal Privman, Christopher P. Childers, Monica C. Munoz-Torres, Jacobus J. Boomsma, Erich Bornberg-Bauer, Cameron R. Currie, Christine G. Elsik, Garret Suen, Michael A. D. Goodisman, Laurent Keller, Juergen Liebig, Alan Rawls, Danny Reinberg, Chris D. Smith, Chris R. Smith, Neil Tsutsui, Yannick Wurm, Evgeny M. Zdobnov, Shelley L. Berger, Juergen Gadau
Article
Multidisciplinary Sciences
Christopher D. Smith, Aleksey Zimin, Carson Holt, Ehab Abouheif, Richard Benton, Elizabeth Cash, Vincent Croset, Cameron R. Currie, Eran Elhaik, Christine G. Elsik, Marie-Julie Fave, Vilaiwan Fernandes, Juergen Gadau, Joshua D. Gibson, Dan Graur, Kirk J. Grubbs, Darren E. Hagen, Martin Helmkampf, Jo-Anne Holley, Hao Hu, Ana Sofia Ibarraran Viniegra, Brian R. Johnson, Reed M. Johnson, Abderrahman Khila, Jay W. Kim, Joseph Laird, Kaitlyn A. Mathis, Joseph A. Moeller, Monica C. Munoz-Torres, Marguerite C. Murphy, Rin Nakamura, Surabhi Nigam, Rick P. Overson, Jennifer E. Placek, Rajendhran Rajakumar, Justin T. Reese, Hugh M. Robertson, Chris R. Smith, Andrew V. Suarez, Garret Suen, Elissa L. Suhr, Shu Tao, Candice W. Torres, Ellen van Wilgenburg, Lumi Viljakainen, Kimberly K. O. Walden, Alexander L. Wild, Mark Yandell, James A. Yorke, Neil D. Tsutsui
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2011)
Article
Multidisciplinary Sciences
Chris R. Smith, Christopher D. Smith, Hugh M. Robertson, Martin Helmkampf, Aleksey Zimin, Mark Yandell, Carson Holt, Hao Hu, Ehab Abouheif, Richard Benton, Elizabeth Cash, Vincent Croset, Cameron R. Currie, Eran Elhaik, Christine G. Elsik, Marie-Julie Fave, Vilaiwan Fernandes, Joshua D. Gibson, Dan Graur, Wulfila Gronenberg, Kirk J. Grubbs, Darren E. Hagen, Ana Sofia Ibarraran Viniegra, Brian R. Johnson, Reed M. Johnson, Abderrahman Khila, Jay W. Kim, Kaitlyn A. Mathis, Monica C. Munoz-Torres, Marguerite C. Murphy, Julie A. Mustard, Rin Nakamura, Oliver Niehuis, Surabhi Nigam, Rick P. Overson, Jennifer E. Placek, Rajendhran Rajakumar, Justin T. Reese, Garret Suen, Shu Tao, Candice W. Torres, Neil D. Tsutsui, Lumi Viljakainen, Florian Wolschin, Juergen Gadau
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2011)
Article
Genetics & Heredity
Garret Suen, Clotilde Teiling, Lewyn Li, Carson Holt, Ehab Abouheif, Erich Bornberg-Bauer, Pascal Bouffard, Eric J. Caldera, Elizabeth Cash, Amy Cavanaugh, Olgert Denas, Eran Elhaik, Marie-Julie Fave, Juergen Gadau, Joshua D. Gibson, Dan Graur, Kirk J. Grubbs, Darren E. Hagen, Timothy T. Harkins, Martin Helmkampf, Hao Hu, Brian R. Johnson, Jay Kim, Sarah E. Marsh, Joseph A. Moeller, Monica C. Munoz-Torres, Marguerite C. Murphy, Meredith C. Naughton, Surabhi Nigam, Rick Overson, Rajendhran Rajakumar, Justin T. Reese, Jarrod J. Scott, Chris R. Smith, Shu Tao, Neil D. Tsutsui, Lumi Viljakainen, Lothar Wissler, Mark D. Yandell, Fabian Zimmer, James Taylor, Steven C. Slater, Sandra W. Clifton, Wesley C. Warren, Christine G. Elsik, Christopher D. Smith, George M. Weinstock, Nicole M. Gerardo, Cameron R. Currie
Article
Biochemistry & Molecular Biology
Jan Buellesbach, Brian A. Whyte, Elizabeth Cash, Joshua D. Gibson, Kelsey J. Scheckel, Rebecca Sandidge, Neil D. Tsutsui
JOURNAL OF CHEMICAL ECOLOGY
(2018)
Article
Biotechnology & Applied Microbiology
Alice B. Dennis, Gabriel Ballesteros, Stephanie Robin, Lukas Schrader, Jens Bast, Jan Berghoefer, Leo W. Beukeboom, Maya Belghazi, Anthony Bretaudeau, Jan Buellesbach, Elizabeth Cash, Dominique Colinet, Zoe Dumas, Mohammed Errbii, Patrizia Falabella, Jean-Luc Gatti, Elzemiek Geuverink, Joshua D. Gibson, Corinne Hertaeg, Stefanie Hartmann, Emmanuelle Jacquin-Joly, Mark Lammers, Blas Lavandero, Ina Lindenbaum, Lauriane Massardier-Galata, Camille Meslin, Nicolas Montagne, Nina Pairie, Marylene Poirie, Rosanna Salvia, Chris R. Smith, Denis Tagu, Sophie Tares, Heiko Vogel, Tanja Schwander, Jean-Christophe Simon, Christian C. Figueroa, Christoph Vorburger, Fabrice Legeai, Juergen Gadau
Article
Evolutionary Biology
Jan Philip Oeyen, Patrice Baa-Puyoulet, Joshua B. Benoit, Leo W. Beukeboom, Erich Bornberg-Bauer, Anja Buttstedt, Federica Calevro, Elizabeth Cash, Hsu Chao, Hubert Charles, Mei-Ju May Chen, Christopher Childers, Andrew G. Cridge, Peter Dearden, Huyen Dinh, Harsha Vardhan Doddapaneni, Amanda Dolan, Alexander Donath, Daniel Dowling, Shannon Dugan, Elizabeth Duncan, Elena N. Elpidina, Markus Friedrich, Elzemiek Geuverink, Joshua D. Gibson, Sonja Grath, Cornelis J. P. Grimmelikhuijzen, Ewald Grosse-Wilde, Cameron Gudobba, Yi Han, Bill S. Hansson, Frank Hauser, Daniel S. T. Hughes, Panagiotis Ioannidis, Emmanuelle Jacquin-Joly, Emily C. Jennings, Jeffery W. Jones, Steffen Klasberg, Sandra L. Lee, Peter Lesny, Mackenzie Lovegrove, Sebastian Martin, Alexander G. Martynov, Christoph Mayer, Nicolas Montagne, Victoria C. Moris, Monica Munoz-Torres, Shwetha Canchi Murali, Donna M. Muzny, Brenda Oppert, Nicolas Parisot, Thomas Pauli, Ralph S. Peters, Malte Petersen, Christian Pick, Emma Persyn, Lars Podsiadlowski, Monica F. Poelchau, Panagiotis Provataris, Jiaxin Qu, Maarten J. M. F. Reijnders, Bjoern Marcus von Reumont, Andrew J. Rosendale, Felipe A. Simao, John Skelly, Alexandros G. Sotiropoulos, Aaron L. Stahl, Megumi Sumitani, Elise M. Szuter, Olivia Tidswell, Evangelos Tsitlakidis, Lucia Vedder, Robert M. Waterhouse, John H. Werren, Jeanne Wilbrandt, Kim C. Worley, Daisuke S. Yamamoto, Louis van de Zande, Evgeny M. Zdobnov, Tanja Ziesmann, Richard A. Gibbs, Stephen Richards, Masatsugu Hatakeyama, Bernhard Misof, Oliver Niehuis
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biology
Aaron F. Pomerantz, Radwanul H. Siddique, Elizabeth Cash, Yuriko Kishi, Charline Pinna, Kasia Hammar, Doris Gomez, Marianne Elias, Nipam H. Patel
Summary: The study used confocal and electron microscopy to examine the glasswing butterfly’s wing development, revealing a reduction in scale precursor cell density and differences in cytoskeletal organization during scale growth between transparent and non-transparent regions. The nanostructures on the wing membrane surface were found to consist of nipple-like structures and wax-based nanopillars, predominantly composed of long-chain n-alkanes, which play a role in generating anti-reflective properties. The findings shed light on the morphogenesis and composition of microstructures and nanostructures, offering potential for new bioinspired anti-reflective materials.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2021)
Article
Biology
Brian A. Whyte, Rebecca Sandidge, Jan Buellesbach, Elizabeth I. Cash, Kelsey J. Scheckel, Joshua D. Gibson, Neil D. Tsutsui
Summary: This study aims to explore if differences in CHCs can explain the differential desiccation survival of Argentine ants. The results showed that most CHCs had a negative correlation with desiccation survival, regardless of compound class. The study suggests that CHC differences between Argentine ant nests are insufficient to explain their desiccation survival.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2023)