Article
Biochemistry & Molecular Biology
Hua Su, Jiahui Xu, Jia Li, Zhenzhen Yi
Summary: The actin gene family is a diverse and ancient eukaryotic cellular cytoskeletal gene family that is essential for many cellular processes. We analyzed the evolutionary pattern of this gene family in ciliates and found that there are ciliate-specific subfamilies of actin genes and the number of actin isoforms varies greatly among ciliate species. The evolution of the actin gene family in ciliates can be explained by the "birth and death" model, and actin genes have been subjected to strong negative selection to maintain their structures and functions.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Janaina Lima de Oliveira, Atahualpa Castillo Morales, Laurence D. Hurst, Araxi O. Urrutia, Christopher R. L. Thompson, Jason B. Wolf
Summary: Studies have found that synonymous codons are used at different frequencies due to the effects of neutral and selective forces. Selection in highly expressed genes remains to be extensively studied, with some evidence suggesting that certain factors do not impact codon preference.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Fang Wang, Yonas I. Tekle
Summary: The evolution and diversity of the Amoebozoa supergroup is complex and poorly understood. Natural selection plays a crucial role in its evolution, and there is heterogeneity in selection across different lineages, potentially related to their ecological environment and adaptation optimization.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Virology
Dimpal A. Nyayanit, Pragya D. Yadav, Rutuja Kharde, Sarah Cherian
Summary: This study provides a comprehensive analysis of codon usage bias in viruses of the Coronaviridae family, revealing the relationship between codon optimization and natural selection, as well as a higher bias in codon usage of the spike gene. The structural genes were found to be significantly influenced by natural selection.
Article
Plant Sciences
Yao Zhang, Zenan Shen, Xiangrui Meng, Liman Zhang, Zhiguo Liu, Mengjun Liu, Fa Zhang, Jin Zhao
Summary: This study investigated the CUB patterns and characteristics of Rosales species, revealing that natural selection is the main factor affecting CUB. Additionally, CUB analysis is an effective method for studying evolutionary relationships among species at the family or order level.
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
Evolutionary Biology
Atahualpa Castillo Morales, Alan M. Rice, Alexander T. Ho, Christine Mordstein, Stefanie Muhlhausen, Samir Watson, Laura Cano, Bethan Young, Grzegorz Kudla, Laurence D. Hurst
Summary: The study reveals the presence of intrahost selection on different types of mutations in SARS-CoV-2, including selection against nonsense, missense, and possibly synonymous mutations. This finding has important implications for methods of mutation rate estimation, determining times to common ancestry, and the potential for intrahost evolution (including vaccine escape).
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Konrad Pawlak, Pawel Blazej, Dorota Mackiewicz, Pawel Mackiewicz
Summary: Synonymous codon usage is influenced by mutations and selection at both the nucleotide and amino acid levels. The proposed mutation-selection model demonstrates that the selection of amino acids based on physicochemical properties can result in biases in codon usage. Alternative genetic codes tend to exhibit greater codon bias than the standard genetic code, and the mutational pressures on cytosine and guanine content further affect usage bias. The study emphasizes the importance of considering amino acid selection in understanding codon usage patterns.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Genetics & Heredity
Anuj Sharma, Shelly Gupta, Karan Paul
Summary: This study compared the preferred codons, codon usage patterns, dinucleotide and amino acid usage patterns of 76 species of the genus Clostridium. It was found that pathogenic Clostridium species had smaller genome sizes with lower AT-rich content, and their choice of codons was influenced by genomic GC/AT content. Pathogenic species displayed a strict bias in codon usage, employing 35 out of 61 codons encoding for 20 amino acids. They also used amino acids with lower biosynthetic cost. Overall, pathogenic members of the genus Clostridium preferred small, AT-rich codons to reduce biosynthetic costs and match the cellular environment of their AT-rich human host.
Article
Virology
Zhen He, Shiwen Ding, Jiyuan Guo, Lang Qin, Xiaowei Xu
Summary: This study analyzed the phylogeny and codon usage pattern of narcissus viruses using the coat protein. The results showed that codon usage bias in these viruses is mainly influenced by natural selection, indicating the importance of evolutionary-based design for controlling these viruses.
Article
Multidisciplinary Sciences
Mebeaselassie Andargie, Zhu Congyi
Summary: This study analyzed the factors shaping codon usage in sesame and identified characteristic codons. There is a relationship between protein length and codon usage, and lignan biosynthesis-related genes show a weaker codon usage bias.
Article
Biology
Tarikul Huda Mazumder, Ali M. Alqahtani, Taha Alqahtani, Talha Bin Emran, Afaf A. Aldahish, Arif Uddin
Summary: The research evaluated codon usage bias in the FoxP2 gene across fishes, birds, reptiles, and mammals, finding that different animal groups prefer specific codon endings based on nucleotide composition. The study suggested that mutation pressure and natural selection may both play a role in influencing codon usage patterns, with mutation pressure having a key influence. Additionally, the base composition under mutation bias affects the codon usage of the FoxP2 gene, while natural selection appears to have a major role over mutation pressure in shaping codon usage bias.
Article
Neurosciences
Rekha Khandia, Mohd. Saeed, Ahmed M. Alharbi, Ghulam Md. Ashraf, Nigel H. Greig, Mohammad Amjad Kamal
Summary: Codon usage analysis is important for molecular characterization and understanding gene evolution. This study investigated the association between gene length and various parameters related to codon usage. The findings showed a significant correlation between gene length and codon bias in neurodegeneration-associated genes. However, this association varied depending on the size of gene segments. The study also found that gene length was associated with nucleotide disproportion and codon choices. This analysis provides insights into gene expression and potential interventions in defective gene functioning in clinical settings.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Agronomy
Huan Hu, Boran Dong, Xiaoji Fan, Meixia Wang, Tingzhang Wang, Qingpo Liu
Summary: This study reveals a significant difference in synonymous codon usage between single-exon genes (SEGs) and multiple-exon genes (MEGs) in rice, accounting for only 2.61% of the total codon usage variability. SEGs and MEGs have distinct base compositions and are under different selective constraints, with SEGs having higher GC content and evolving relatively faster. Variability in synonymous codon usage among SEGs is influenced by variations in GC content, gene function, and gene expression level. These findings deepen our understanding of the mechanisms behind the origin, differentiation, and regulation of SEGs in plants.
Article
Biology
Gabriel de Moura Silva, Daniel J. G. Lahr, Rosana Louro Ferreira Silva
Summary: This article presents the importance of educational resources designed by undergraduate students in teaching diversity and animal evolution. The creation and analysis of these resources can help to develop evolutionary thinking and enhance the design of teaching-learning sequences.
JOURNAL OF BIOLOGICAL EDUCATION
(2023)
Article
Microbiology
Fatma Gomaa, Daniel R. Utter, Wesley Loo, Daniel J. G. Lahr, Colleen M. Cavanaugh
Summary: Research on protist-bacteria interactions is important for understanding their roles in ecosystems and human health. This study focuses on the specificity and diversity of microbial communities associated with the testate amoeba Arcella spp. The results show that the associations between Arcella and bacteria are species-specific, and each host Arcella species has a distinct bacterial composition.
EUROPEAN JOURNAL OF PROTISTOLOGY
(2022)
Review
Microbiology
Caitlin M. Timmons, Shahed U. A. Shazib, Laura A. Katz
Summary: Mobile genetic elements play important roles in evolution by influencing genome structure and molecular evolution, providing adaptive advantages and genetic diversity, as well as altering host cell defense mechanisms against viral pathogens.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2022)
Review
Microbiology
Ragib Ahsan, Wumei Blanche, Laura A. Katz
Summary: Ciliates are characterized by the presence of two types of nuclei, germline micronucleus and somatic macronucleus, which vary in size and structure among different ciliate species. The macronucleus contains transcriptionally active chromosomes that differ in size between ciliate classes, while the micronucleus is transcriptionally inactive and contains canonical chromosomes inherited between generations. This study explores the diversity in somatic macronuclear architecture across different ciliate lineages, with a focus on lineages with extensively fragmented chromosomes. It also synthesizes information on ciliate macronuclear development and highlights the diversity among ciliate nuclear cycles, providing insights into genome evolution and nuclear features in eukaryotes.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2022)
Article
Microbiology
Agnes K. M. Weiner, Billie Cullison, Shailesh Date, Tomas Tyml, Jean-Marie Volland, Tanja Woyke, Laura A. Katz, Robin S. Sleith
Summary: The study analyzed the genetic diversity of Chlorella algae in the amoeba species Hyalosphenia papilio, revealing the diversity of this host-symbiont association and the transient nature of their symbiosis. The analysis also showed that the algal nuclei are inactive, suggesting that the algae may be temporarily exploited for photosynthetic activity before being digested.
Article
Environmental Sciences
Wenping Wang, Xiaofei Gao, Jean Claude Ndayishimiye, Enrique Lara, Daniel J. G. Lahr, Haifeng Qian, Kexin Ren, Huihuang Chen, Jun Yang
Summary: Research has shown that rising temperatures significantly affect the population changes of the sensitive species N. tuberspinifera, with transcriptomic analysis revealing different molecular responses at various temperatures. The study also found that N. tuberspinifera is unable to survive when temperatures exceed 40 degrees Celsius.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Editorial Material
Evolutionary Biology
Adam Eyre-Walker, Laura A. Katz
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Rabindra Thakur, Adena B. Collens, Mattia Greco, Robin S. Sleith, Jean-David Grattepanche, Laura A. Katz
Summary: This article presents a metabarcoding survey of foraminiferal diversity using newly designed foraminifera-specific primers. The study shows that the majority of foraminifera species remain unidentified, and identifies distinct habitat preferences among the observed species.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2022)
Article
Evolutionary Biology
Mario A. Ceron-Romero, Miguel M. Fonseca, Leonardo de Oliveira Martins, David Posada, Laura A. Katz
Summary: Based on gene tree parsimony analysis, we suggest that the root of the eukaryotic tree of life may lie between Opisthokonta and all other eukaryotes, but there is still uncertainty. Further analysis of genome size supports this viewpoint.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Giulia M. Ribeiro, Daniel J. G. Lahr
Summary: Arsenic is an omnipresent element that exerts constant evolutionary pressure on organisms. While the arsenic resistance machinery is well described in bacteria, our understanding of its evolution in eukaryotes is limited. In this study, we investigated the origin and evolution of core arsenic resistance genes in eukaryotes using a wide phylogenetic framework. Our findings suggest that arsenic resistance mechanisms are likely ancestral to eukaryotes and have been subject to gene duplication and horizontal gene transfer. Despite the significant contribution of horizontal gene transfer to the expansion of arsenic metabolism in eukaryotes, we propose the hypothesis of ancestral origin and differential retention of arsenic resistance mechanisms in this group.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Ruben Gonzalez-Miguens, Milcho Todorov, Quentin Blandenier, Clement Duckert, Alfredo L. Porfirio-Sousa, Giulia M. Ribeiro, Diana Ramos, Daniel J. G. Lahr, David Buckley, Enrique Lara
Summary: In this study, the authors used Arcellinida testate amoebae as a model to test the paradigm of morphological stasis in protists. The results showed a lack of conservatism in shell outlines and widespread morphological convergences between far-related taxa. In addition, the authors revised the systematics and established a new infraorder and two new genera.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Simon Roux, Matthias G. Fischer, Thomas Hackl, Laura A. Katz, Frederik Schulz, Natalya Yutin
Summary: Virophages are small dsDNA viruses that hijack the machinery of giant viruses during co-infection and play a unique role in the viral world. However, the lack of clarity in nomenclature and taxonomy has hindered further studies on virophages and related viruses. In this study, we propose delineation criteria and classification methods for virophages based on comparative genomics and phylogenetic analysis, establishing a taxonomic framework for this group of viruses. This classification provides a necessary first step for future research in this field.
Article
Biochemistry & Molecular Biology
Ruben Gonzalez-Miguens, Emilio Cano, Antonio Guillen-Oterino, Antonio Quesada, Daniel J. G. Lahr, Daniel Tenorio-Rodriguez, David de Salvador-Velasco, David Velazquez, Maria Isabel Carrasco-Braganza, R. Timothy Patterson, Enrique Lara, David Singer
Summary: Environmental DNA-based diversity studies have become popular and have made significant contributions to various fields of biology. This study presents a species-level eDNA protocol based on mitochondrial COI gene to explore testate amoeba diversity in lentic water bodies and soil ecosystems. Results revealed unexpected diversity within morphologically homogeneous groups. This protocol has the potential to revolutionize Arccelinida distributional surveys and establish it as a model group for diverse studies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Evolutionary Biology
Leticia Chiara Baldassio de Paula, Rodrigo de Vilhena Perez Dios, Filipe Macedo Gudin, Marcelo Domingos de Santis, Deivys Moises Alvarez-Garcia, Manuel Antunes Junior, Beatriz Vieira Freire, Fernando Portella de Luna Marques, Daniel Jose Galafasse Lahr, Silvio Shigueo Nihei
Summary: Tachinidae is the second largest and species-rich family in Diptera, with all members being parasitoids. This study presents the first phylogenomic analysis of Tachinidae using transcriptomic data, revealing the subfamilial relationships and the existence of a fifth lineage.
Article
Ecology
Agnes K. M. Weiner, Taylor Sehein, Auden Cote-L'Heureux, Robin S. Sleith, Mattia Greco, Clara Malekshahi, Chase Ryan-Embry, Naomi Ostriker, Laura A. Katz
Summary: The study investigates the population genetics of uncultivable heterotrophic protists using transcriptomics data. The researchers analyze multiple genes from two morphospecies of testate amoebae and confirm the existence of cryptic species with evidence of recombination and high levels of divergence. However, the total levels of genetic diversity within cryptic species are low, suggesting small effective population sizes and efficient modes of dispersal.