Article
Virology
Jiazheng Xie, Bowen Tan, Yi Zhang
Summary: Bats have unique biological features and the TRIM family of proteins play important roles in various cellular functions in bats. The study analyzed the composition, evolution, and expression of bat TRIM genes and found potential links to antiviral immunity, longevity, and DNA damage tolerance. These findings provide a theoretical basis for further research on bat TRIM in these areas.
Article
Plant Sciences
Yun-Hai Lu, Intikhab Alam, Yan-Qing Yang, Ya-Cen Yu, Wen-Chao Chi, Song-Biao Chen, Boulos Chalhoub, Li-Xi Jiang
Summary: The YABBY gene family, present in all seed plants, plays crucial roles in plant growth and development, including polarity establishment, leaf and flower formation, and response to hormonal signals and environmental stress. Through identification of 364 YABBY genes in 37 Brassicaceae genomes, it was found that these genes are largely conserved across species but exhibit considerable functional divergence.
Article
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL 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
Biochemical Research Methods
Chaitanya Aluru, Mona Singh
Summary: The study introduces a reconciliation-based framework that considers the relative positions of protein domains within extant sequences to uncover tandem domain duplications accurately. By developing an integer linear programming approach and a heuristic algorithm, the researchers are able to identify single and tandem domain duplication events with high accuracy. Through extensive simulation studies and testing on an orthogroup with complex domain duplication patterns, the effectiveness of the approach is demonstrated.
Article
Biotechnology & Applied Microbiology
Danny Bergeron, Cedric Laforest, Stacey Carpentier, Annabelle Calve, Etienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Michelle S. Scott
Summary: The study reveals that snoRNA copy regulation affects family sizes, genomic location of the members, and controls both member and total family abundance to meet the needs of individual tissues. Additionally, the expression variability of individual snoRNA family members is preferred over the total variability of the family, pointing towards differential regulation mechanisms exist to ensure uniformity of the total family abundance across tissues.
Article
Multidisciplinary Sciences
Javier Gutierrez, Roy Platt, Juan C. Opazo, David A. Ray, Federico Hoffmann, Michael Vandewege
Summary: PIWIs are regulatory proteins that protect germline against transposable elements and are primarily expressed in gonads in vertebrates. The duplication history of Piwi genes is complex, with some genes being retained in all members, while others being derived from duplication events in common ancestors and subsequently lost in certain lineages. Despite two rounds of whole genome duplication in vertebrate evolution, Piwi expansion seems to have occurred independently of these events.
Article
Plant Sciences
Yangyang Wei, Zhaoguo Li, Tom C. Wedegaertner, Susan Jaconis, Sumei Wan, Zilin Zhao, Zhen Liu, Yuling Liu, Juyun Zheng, Kater D. Hake, Renhai Peng, Baohong Zhang
Summary: This study identified and analyzed the PEPC genes in cotton, revealing their presence and differentiation in different sub-genomes. The expression patterns of these genes were also examined during development and under stress conditions, uncovering their importance and functional diversity in cotton evolution.
Article
Multidisciplinary Sciences
Dia A. Ghose, Kaitlyn E. Przydzial, Emily M. Mahoney, Amy E. Keating, Michael T. Laub
Summary: The evolution of novel functions in biology relies on gene duplication and divergence, creating large paralogous protein families. However, the specificity of these paralogs to their interaction partners can be sensitive to mutation. Through deep mutational scanning, it was demonstrated that a family of bacterial signaling proteins exhibits marginal specificity, with individual substitutions leading to substantial cross-talk between pathways. These findings suggest that the evolution of bacterial signaling proteins is constrained by sequence space crowding, and that evolution selects for good enough rather than optimized phenotypes in paralogs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Rachel A. Smoak, Lindsey F. Snyder, Jan S. Fassler, Bin Z. He
Summary: Opportunistic yeast pathogens, such as multidrug-resistant Candida auris, have arisen multiple times in the Saccharomycetes class. The expansion and diversification of adhesin families, particularly the Hyr/Iff-like (Hil) family, contribute to variation in adhesion and virulence within and between Candida species. The rapid divergence and large variations in length and beta-aggregation potential of the adhesin proteins, as well as their enrichment at chromosomal ends, suggest an important role in the emergence of fungal pathogens.
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
Genetics & Heredity
Jinjie Zhao, Xinyuan Pu, Wenfei Li, Meng Li
Summary: This study identified 84 PLD genes in six mosses and analyzed their classification and structure. The results showed that moss PLDs play key roles in stress responsiveness and plant development, and some PLDs were differentially expressed under biotic and abiotic stresses. Episodic positive selection was also found in moss PLDs, which may have facilitated the colonization of land by mosses.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Da Fang, Weimeng Zhang, Xiuzhu Cheng, Fei Hu, Ziyi Ye, Jun Cao
Summary: The SHI/STY genes were classified into four clades with similar motif distribution and gene structure within each clade. SHI/STY proteins are predicted to be localized in the nucleus. The promoters of SHI/STY genes contain different types of cis-elements, suggesting their involvement in various biological processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Fei Hu, Ziyi Ye, Weimeng Zhang, Da Fang, Jun Cao
Summary: This study identified 173 Cupin genes in Brassica napus and analyzed their molecular evolution and expression patterns. These genes were classified into ten groups and showed a high degree of conservation within each group. The expansion of BnaCupins was mainly contributed by whole-genome duplication and segmental duplication events. The study also found that BnaCupins are involved in plant growth and stress responses, and identified some interacting proteins. This research enriches our understanding of the Cupin gene family in B. napus and provides a basis for further functional studies.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Genetics & Heredity
Saara K. Luna, Frederic J. J. Chain
Summary: This study investigated lineage-specific genes and gene family expansions across five dictyostelid species to determine their expression patterns during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression and showed independent functional innovations throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, possibly due to subfunctionalization or neofunctionalization.
Article
Biology
Daniela Tejada-Martinez, Joao Pedro de Magalhaes, Juan C. Opazo
Summary: The study revealed the evolutionary mechanisms of cetaceans against cancer and other diseases, showing that TSGs genes in cetaceans have been affected by positive selection during evolution and have a higher gene turnover rate. These gene variations may contribute to the evolution of cetaceans' traits of anti-cancer resistance, gigantism, and longevity.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Evolutionary Biology
Federico G. Hoffmann, Jay F. Storz, Shigehiro Kuraku, Michael W. Vandewege, Juan C. Opazo
Summary: Globin-X (GbX) is a mysterious member of the vertebrate globin gene family, with potential roles in cellular signaling or protection against lipid oxidation. Research integrates bioinformatics, synteny, and phylogenetic analyses to study the diversity of GbX genes in different species and the impact of whole-genome duplications on vertebrate genomes.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Mycology
Phillip L. Vines, Federico G. Hoffmann, Florencia Meyer, Thomas W. Allen, Maria Tomaso-Peterson
Summary: This study identified a new species within the genus Gaeumannomyces and demonstrated its pathogenicity and ability to infect the roots of ultradwarf bermudagrass.
Article
Multidisciplinary Sciences
Juan C. Opazo, Michael W. Vandewege, Javier Gutierrez, Kattina Zavala, Luis Vargas-Chacoff, Francisco J. Morera, Gonzalo A. Mardones
Summary: GOLPH3, the first reported oncoprotein of the Golgi apparatus, has been puzzling in its function in normal and cancer cells since its discovery about 20 years ago. Studying the evolution of the GOLPH3 gene family in birds provides insights into its evolutionary history and importance in structural and functional attributes.
SCIENTIFIC REPORTS
(2021)
Article
Developmental Biology
Juan C. Opazo, Federico G. Hoffmann, Kattina Zavala, Scott Edwards
Summary: The DAN gene family plays fundamental roles in development and is associated with diseases in adulthood. This study investigates the evolutionary history of the DAN gene family in vertebrates, identifying two new gene lineages and reconstructing the ancestral repertoire of DAN genes in gnathostomes.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Michael W. Vandewege, Roy N. I. I. I. I. Patt, Dana K. Merriman, David A. Ray, Federico G. Hoffmann
Summary: The PIWI/piRNA defense system against transposable elements (TEs) is less effective in the absence of actively mobilizing TEs. The study on the 13-lined ground squirrel reveals that while there is no active TE insertion, TEs are still actively transcribed. The Piwi genes are not expressed until after a certain stage of testis development, and there is little change in TE expression with the onset of Piwi expression. This suggests that the PIWI/piRNA system is less efficient in suppressing TE transcription in squirrels compared to mice and rabbits.
Article
Multidisciplinary Sciences
Javier Gutierrez, Roy Platt, Juan C. Opazo, David A. Ray, Federico Hoffmann, Michael Vandewege
Summary: PIWIs are regulatory proteins that protect germline against transposable elements and are primarily expressed in gonads in vertebrates. The duplication history of Piwi genes is complex, with some genes being retained in all members, while others being derived from duplication events in common ancestors and subsequently lost in certain lineages. Despite two rounds of whole genome duplication in vertebrate evolution, Piwi expansion seems to have occurred independently of these events.
Article
Multidisciplinary Sciences
Juan C. Opazo, Kattina Zavala, Luis Vargas-Chacoff, Francisco J. Morera, Gonzalo A. Mardones
Summary: This study investigates the evolutionary dynamics of the TARDBP gene in primates and identifies novel retropseudogenes associated with this gene. It also discovers species-specific retropseudogenes in several primate species.
SCIENTIFIC REPORTS
(2022)
Article
Evolutionary Biology
William Joyce, Daniel M. Ripley, Todd Gillis, Amanda Coward Black, Holly A. Shiels, Federico G. Hoffmann
Summary: The troponin complex, responsible for muscle activation, is composed of three interacting protein subunits: TnC, TnI, and TnT. Through phylogenetic and synteny analysis, we have identified five distinct TNNI classes (TNNI1-5) and four TNNT classes (TNNT1-4) in a diverse array of vertebrates.
GENOME BIOLOGY AND EVOLUTION
(2023)
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)
Letter
Biochemistry & Molecular Biology
Jay F. Storz, Schuyler Liphardt, Marcial Quiroga-Carmona, Naim M. Bautista, Juan C. Opazo, Timothy B. Wheeler, Guillermo D'Elia, Jeffrey M. Good
Article
Fisheries
Danixa Martinez, Daniela Nualart, Carlos Loncoman, Juan C. Opazo, Kattina Zabala, Francisco J. Morera, Gonzalo A. Mardones, Luis Vargas-Chacoff
Summary: This study investigates the role of HMG proteins in the immune response of fish, specifically focusing on BbX protein. The results show that BbX protein is highly expressed in the intestinal tissue and liver of E. maclovinus. In addition, BbX protein expression levels increase in response to P. salmonis injection and thermal stress. These findings suggest that BbX protein may play a role in the response mechanism to temperature and bacterial stimulation in fish.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2023)
