Article
Biochemistry & Molecular Biology
R. Axel W. Wiberg, Jeremias N. Brand, Lukas Schaerer
Summary: Our study reveals that reproductive-related genes in hermaphroditic animals of the Macrostomum genus evolve faster than widely expressed genes, indicating stronger sexual selection on the former. Additionally, species with hypodermic sperm morphologies show elevated molecular sequence evolution, regardless of a gene's functional annotation. These findings suggest reduced selection efficiency following shifts to hypodermic mating, possibly due to higher selfing rates in these species.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Mitchell J. Syberg-Olsen, Arkadiy Garber, Patrick J. Keeling, John P. McCutcheon, Filip Husnik
Summary: Pseudofinder is an open-source software for detecting and analyzing pseudogenes in bacterial and archaeal genomes. The software's multi-pronged, reference-based approach allows it to detect a wide variety of pseudogenes, including highly degraded ones missed by gene-calling pipelines, as well as newly formed pseudogenes with few inactivating mutations. Additionally, Pseudofinder can identify genes that lack inactivating substitutions but experience relaxed selection. Implementation of Pseudofinder in annotation pipelines enables more precise estimation of the functional potential of sequenced microbes and generates new hypotheses about the evolutionary dynamics of bacterial and archaeal genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Plant Sciences
Sariel Huebner
Summary: Graph-based pangenomes can provide a comprehensive platform to study diversity in populations or species, but still face challenges in species with large complex genomes. However, with advancing technology, the graph-pangenome is expected to become a central platform in genomics studies and applications.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Parul Johri, Susanne P. Pfeifer, Jeffrey D. Jensen
Summary: Building appropriate baseline models for natural populations helps answer fundamental questions in population genetics and identify candidate loci experiencing rare and episodic forms of selection. A baseline model was developed for a human population of West African ancestry, the Yoruba, taking into account various evolutionary processes. An approximate Bayesian approach was used to infer population growth and distribution of fitness effects, suggesting weak to moderate positive selection that is consistent but difficult to identify if rare.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Biochemistry & Molecular Biology
Koji Arikawa, Masahito Hosokawa
Summary: Due to the limitations of traditional culture techniques, culture-independent analyses have become essential for studying microbial ecology and function. This mini-review focuses on the methods of metagenomics and single-cell genomics for obtaining genetic information from uncultured prokaryotes and discusses their advantages and limitations. Recent advancements in technology and data analysis have the potential to overcome current challenges and facilitate a deeper understanding of uncultured microbial ecosystems and "microbial dark matter" genes and proteins.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Microbiology
Masato Kogawa, Yohei Nishikawa, Tatsuya Saeki, Takuya Yoda, Koji Arikawa, Haruko Takeyama, Masahito Hosokawa
Summary: Single-cell genomics is a promising approach for studying uncultured bacteria. In this study, a single-cell amplified genome long-read assembly (scALA) workflow was developed to construct complete circular single-amplified bacterial genomes. Through scALA, 16 complete circular genomes of specific bacteria were obtained from human fecal samples, providing insights into microbial evolution, adaptation to environmental changes, and interactions with hosts.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Damariz Gonzalez, Mauricio Morales-Olavarria, Boris Vidal-Veuthey, Juan P. Cardenas
Summary: This study provides insights into the evolutionary adaptation of Akkermansia to the gastrointestinal niche. The results reveal that Akkermansia have open pangenomes and genes associated with mucin degradation and microbial interactions are closely related to the origin of the genus. Furthermore, the evolutionary patterns of Akkermansia species vary and mucin degradation is identified as an essential feature in the evolution of this symbiotic species.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Michael Westbury, Diana Le Duc, David A. Duchene, Arunkumar Krishnan, Stefan Prost, Sereina Rutschmann, Jose H. Grau, Love Dalen, Alexandra Weyrich, Karin Noren, Lars Werdelin, Fredrik Dalerum, Torsten Schoeneberg, Michael Hofreiter
Summary: During the Miocene, the highly diverse family of Carnivora, Hyaenidae, has been reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage was found, with high levels of genetic diversity and stable population sizes seen in the spotted hyena and aardwolf.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Carlos Caicedo-Montoya, Maria Paula Gomez-Roman, Melissa Vazquez-Hernandez, Ricardo Alexis Mora-Rincon, Stefany Daniela Rodriguez-Luna, Romina Rodriguez-Sanoja, Sergio Sanchez
Summary: Actinobacteria, known for their high GC content and production of antimicrobials, have genomes rich in novel secondary metabolites with biotechnological potential. Three novel plant isolates were analyzed, revealing adaptions to their habitats, evolutionary patterns, and potential secondary metabolite production. The isolates exhibited positively selected genes related to stress resistance and biosynthesis of secondary metabolites, providing avenues for future research on bioactive compound characterization.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lin Yang, Fuwen Wei, Xiangjiang Zhan, Huizhong Fan, Pengpeng Zhao, Guangping Huang, Jiang Chang, Yinghu Lei, Yibo Hu
Summary: This study investigates the genomics of takins and reveals the existence of two phylogenetic species and recent speciation. Two genetically divergent subspecies were also identified. The findings provide insights into the scientific conservation of takins and the biogeography of the Himalaya-Hengduan biodiversity hotspot.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Qin Qiao, Patrick P. Edger, Li Xue, La Qiong, Jie Lu, Yichen Zhang, Qiang Cao, Alan E. Yocca, Adrian E. Platts, Steven J. Knapp, Marc Van Montagu, Yves Van de Peer, Jiajun Lei, Ticao Zhang
Summary: Strawberry has become a model system for various research, with genomes of five different species sequenced in recent years. A study reported chromosome-scale reference genomes for five strawberry species, along with genome resequencing data for 128 additional accessions, providing valuable resources for future studies. The research also identified a new diploid species and explored the evolutionary dynamics of gene families, pointing out mutations associated with white pigmented fruit in different strawberry species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Zhiqiang Han, Manhong Liu, Qi Liu, Hao Zhai, Shijun Xiao, Tianxiang Gao
Summary: The burbot, adapted solely to freshwater, has the widest longitudinal range among freshwater fish worldwide. A high-quality chromosome-level genome of burbot was constructed using PacBio long sequencing and Hi-C technology, providing valuable insights for ecological and evolutionary studies within the order Gadiformes.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Ecology
Carrie A. Whittle, Arpita Kulkarni, Cassandra G. Extavour
Summary: Sex-biased gene expression, particularly in the gonad, is associated with accelerated protein sequence evolution in the hemimetabolous insect Gryllus bimaculatus. Sex-biased brain genes also exhibit rapid protein sequence evolution, more pronounced in females, and are linked to sexual functions and mating behaviors. Narrow tissue expression breadth and relaxed purifying selection for sex-biased brain genes may provide enhanced freedom for adaptive protein functional changes.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Plant Sciences
Nathaniel J. J. Klimpert, Juliana Lischka Sampaio Mayer, Deise Schroder Sarzi, Francisco Prosdocimi, Fabio Pinheiro, Sean W. W. Graham
Summary: The study reveals Pogoniopsis as an independent case of photosynthesis loss in orchids and provides insights into its molecular evolution at the genomic level. Slowly evolving mitochondrial genes help clarify the phylogenetic placement of Pogoniopsis in orchids, contrasting with the rate-elevated plastome data.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Virology
Chiara Arcangeli, Martina Torricelli, Carla Sebastiani, Daniele Lucarelli, Marcella Ciullo, Fabrizio Passamonti, Monica Giammarioli, Massimo Biagetti
Summary: The study genetically characterized SRLVs circulating in central Italy, revealing the presence of genotypes A and B in the samples, with no recombination events detected. Mutations were mainly localized in the VR-2 region, and the dN/dS ratio indicated the existence of purifying selection.
Article
Environmental Sciences
Frank O. Aylward
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2021)
Article
Virology
Frank O. Aylward, Mohammad Moniruzzaman
Summary: Giant viruses, also known as NCLDVs, are prevalent in the biosphere and play crucial roles in biogeochemical cycling and host genome evolution. They have been found to be abundant in metagenomic datasets and their sequences can be endogenized in various eukaryotic genomes. The accurate detection of NCLDV sequences is challenging due to sequence divergence and gene diversity, but ViralRecall, a bioinformatic tool, has been developed for this purpose with high sensitivity and specificity. It can be useful in removing contaminating sequences in metagenome-assembled viral genomes and identifying eukaryotic genomic loci derived from NCLDVs.
Article
Microbiology
Sangita Karki, Mohammad Moniruzzaman, Frank O. Aylward
Summary: The Asfarviridae family is a diverse and cosmopolitan group of viruses, with high genomic divergence across different members and a broad environmental distribution in marine, freshwater, and terrestrial habitats. They encode genes with diverse predicted metabolic roles and show genomic chimerism, with some members potentially infecting ecologically important protists in the ocean.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ecology
Daniel Muratore, Angela K. Boysen, Matthew J. Harke, Kevin W. Becker, John R. Casey, Sacha N. Coesel, Daniel R. Mende, Samuel T. Wilson, Frank O. Aylward, John M. Eppley, Alice Vislova, Shengyun Peng, Rogelio A. Rodriguez-Gonzalez, Stephen J. Beckett, E. Virginia Armbrust, Edward F. DeLong, David M. Karl, Angelicque E. White, Jonathan P. Zehr, Benjamin A. S. Van Mooy, Sonya T. Dyhrman, Anitra E. Ingalls, Joshua S. Weitz
Summary: By integrating time series analyses of different molecules, the authors demonstrate that microorganisms in the open ocean partition scarce resources temporally, with different microbial groups expressing nitrogen uptake and assimilation processes at different points throughout the day and night cycle. Despite competition for limited nutrients, high taxonomic diversity of microbes in the surface ocean still persists, which challenges ecological theory. The study reveals temporal niche partitioning of nitrogen assimilation processes, with different microbial groups exhibiting asynchronous transcription of genes involved in nitrogen uptake.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Ecology
Alaina R. Weinheimer, Frank O. Aylward
Summary: Recent research has highlighted the significant diversity and importance of large DNA viruses in the marine environment. However, detecting these viruses can be challenging due to their large size and complex genomes. In this study, the genomic diversity and distribution of jumbo bacteriophages in the ocean were assessed using metagenomic data. The findings reveal that jumbo phages are widespread in the ocean and exhibit complex genomic repertoires and ecological impacts.
Article
Genetics & Heredity
Carolina A. Martinez-Gutierrez, Frank O. Aylward
Summary: The evolutionary forces determining genome size in bacteria and archaea have been debated for decades. This study suggests that there is a strong phylogenetic signal in genome size distributions at broad phylogenetic scales, despite the ability of bacteria and archaea to exchange genes rapidly.
Review
Biochemistry & Molecular Biology
Frank O. Aylward, Mohammad Moniruzzaman
Summary: Discoveries over the last century have shown that viruses can be surprisingly complex in terms of their physical structures, genomic organization, ecological interactions, and evolutionary histories. They can have physical dimensions and genome lengths that surpass many cellular lineages, and their infection strategies often involve significant remodeling of their host cells. Virus-virus communication and hyperparasitism are common in the virosphere, contributing to their success. The study of large DNA viruses is particularly important for understanding viral complexity and future research directions.
Article
Virology
Mohammad Moniruzzaman, Maria P. Erazo-Garcia, Frank O. Aylward
Summary: This study discovered the presence of endogenous giant viruses in Chlamydomonas reinhardtii, which has important implications for understanding the genetic characteristics and population dynamics of this alga.
Editorial Material
Multidisciplinary Sciences
Mohammad Moniruzzaman, Frank O. Aylward
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Justus Niemeyer, Laura Fischer, Frank O'Neill Aylward, Michael Schroda
Summary: This study investigated the use of promoters from giant virus genomes in Chlamydomonas reinhardtii to drive gene expression. The results showed that the viral promoters were unable to effectively drive gene expression. Additionally, it was found that by mutating the start codons of mCherry and using the 5 '-UTR of beta TUB2, the problem of gene expression in Chlamydomonas could be overcome.
Correction
Microbiology
Angela K. Boysen, Laura T. Carlson, Bryndan P. Durham, Ryan D. Groussman, Frank O. Aylward, Francois Ribalet, Katherine R. Heal, Angelicque E. White, Edward F. DeLong, E. Virginia Armbrust, Anitra E. Ingalls
Article
Virology
Frank O. Aylward, Jonatas S. Abrahao, Corina P. D. Brussaard, Matthias G. Fischer, Mohammad Moniruzzaman, Hiroyuki Ogata, Curtis A. Suttle
Summary: Recent taxonomic updates have been made for giant viruses in the order Imitervirales, including the creation of new families and subfamilies, as well as the adoption of binomial names for all recognized species.
ARCHIVES OF VIROLOGY
(2023)
Article
Ecology
Anh D. D. Ha, Mohammad Moniruzzaman, Frank O. O. Aylward
Summary: Viruses of the phylum Nucleocytoviricota are widespread in ocean waters and have important impacts on marine ecosystems. This study used metagenomic data to investigate the biogeography of these viruses and found that they are most abundant in shallow waters. The study also identified latitudinal patterns in viral diversity, with the highest diversity observed at high latitudes in the northern hemisphere. These results contribute to our understanding of the distribution and diversity of viruses in marine systems.
ISME COMMUNICATIONS
(2023)
Article
Ecology
Alaina R. Weinheimer, Frank O. Aylward, Matthieu Leray, Jarrod J. Scott
Summary: Phages play a crucial role in controlling microbial communities by selectively infecting and killing cells. The composition of phage communities is primarily shaped by dispersal processes, while prokaryotes are more influenced by local conditions.
ISME COMMUNICATIONS
(2023)
Review
Microbiology
Mohammad Moniruzzaman, Maria Paula Erazo Garcia, Roxanna Farzad, Anh D. Ha, Abdeali Jivaji, Sangita Karki, Uri Sheyn, Joshua Stanton, Benjamin Minch, Danae Stephens, Dustin C. Hancks, Rodrigo A. L. Rodrigues, Jonatas S. Abrahao, Assaf Vardi, Frank O. Aylward
Summary: The phylum Nucleocytoviricota includes the largest and most complex viruses known, with a long evolutionary history. These viruses manipulate the physiology of their hosts, including through mimicry and the acquisition of various functional genes. Understanding the roles of viral genes during infection and how viruses acquire complex functional repertoires are important areas of research in giant virus studies.
FEMS MICROBIOLOGY REVIEWS
(2023)