Article
Biochemical Research Methods
Panagiotis Moulos
Summary: This article introduces a software package called recoup, which can visualize genomic coverage profiles generated from Next Generation Sequencing data quickly, flexibly, comprehensively, while also considering ease of use and reusability.
BMC BIOINFORMATICS
(2021)
Article
Fisheries
Senyuan Li, Liqiong Xu, Yuhong Shi, Jiong Chen
Summary: By using the 2b-RAD-seq method, the study identified the sex determination mechanism of ayu fish, isolated male-specific scaffolds, and supported an XX/XY sex determination system in ayu. The multiplex-PCR assay based on male-specific markers was developed for molecular sexing in ayu culture.
Article
Biochemistry & Molecular Biology
Nicola Zilio, Helle D. Ulrich
Summary: Mapping the genome-wide distribution of single-strand breaks is crucial for understanding damage signaling and DNA repair. This article reviews classical and newly developed high-resolution methods for mapping single-strand breaks, highlighting the valuable insights they provide into the impact of this type of damage on the genome.
Article
Biochemistry & Molecular Biology
Nicolas C. Rochette, Angel G. Rivera-Colon, Jessica Walsh, Thomas J. Sanger, Shane C. Campbell-Staton, Julian M. Catchen
Summary: Library preparation protocols for most sequencing technologies involve PCR amplification, which may lead to PCR duplicates and affect the reliability of experiments. In this study, a general quantitative model is developed to investigate the factors controlling the occurrence of PCR duplicates. It is found that the PCR duplicate rate is primarily determined by the ratio between library complexity and sequencing depth. The proposed framework provides a method to estimate library complexity and amplification noise in any data set containing PCR duplicates, and also discusses the impact of amplification-related artefacts on downstream analyses.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Environmental Sciences
Tessa M. Page, Jonathan W. Lawley
Summary: As we enter the United Nations Decade of Ocean Science for Sustainable Development, efforts to reverse ocean health decline are urgent. Transcriptomic technologies are playing an increasingly important role in marine ecology research, providing researchers with valuable tools to understand genetic variation, cellular processes, and pathways.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Forestry
Zoltan A. Kobolkuti, Endre Gy. Toth, Zsolt Keseru, John H. Fike, Bence Bolla, Tamas Abri, Attila Borovics, Attila Benke, Klara Cseke
Summary: Robinia pseudoacacia, commonly known as black locust, is an economically and environmentally important plant native to the eastern USA and introduced to European countries. By using genome-wide genetic data, this study aims to identify gene variants with functional effects on complex traits and evaluate breeding efforts. Highly variable SNP markers from native American and Hungarian individuals are provided, which can be used for genetic differentiation assessment and further research into this species.
TREE GENETICS & GENOMES
(2023)
Article
Biochemistry & Molecular Biology
Christos Tzaferis, Evangelos Karatzas, Fotis A. Baltoumas, Georgios A. Pavlopoulos, George Kollias, Dimitris Konstantopoulos
Summary: Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single-cell resolution remain challenges in the biomedical field. SCALA is a bioinformatics tool for analyzing and visualizing single-cell RNA sequencing and Assay for Transposase-Accessible Chromatin using sequencing data-sets. It offers independent or integrative analysis options and various analysis modules to aid biomedical researchers in exploring, analyzing, and visualizing their data without coding experience.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Plant Sciences
Jill C. Preston
Summary: The development of plant model organisms is traditionally analyzed using resource-heavy, tailored applications that are not easily transferable to non-model taxa. Next-generation sequencing (NGS) is increasingly becoming a powerful tool in evolutionary developmental biology (evo-devo) studies. Plant biologists are utilizing natural diversity for crop improvement, enhancing ecosystem functioning, and better understanding plant responses to climate change.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Virology
Zilei Zhang, Danlei Liu, Dapeng Wang, Qingping Wu
Summary: The study introduced a new method called TRACE-seq for preparing next generation sequencing libraries for Human noroviruses (HuNoVs), allowing almost complete viral genome attainment and demonstrating high reliability and versatility.
Article
Ecology
Luis Albero, Inigo Martinez-Solano, Miguel Hermida, Manuel Vera, Pedro Tarroso, Eloy Becares
Summary: This study assessed the functional connectivity of the sharp ribbed newt populations in an agricultural landscape in NW Spain. The results showed that open areas, such as rainfed crops and grasslands, play an important role in promoting gene flow and functional connectivity between amphibian populations. Conservation policies should adopt a functional network strategy to protect interconnected temporary ponds across the traditional agricultural matrix.
Article
Biology
Roberto Vera Alvarez, Lorinc Pongor, Leonardo Marino-Ramirez, David Landsman
Summary: PM4NGS is a project management framework for NGS data analysis, providing a standard organizational structure, bioinformatics tool management, and data analysis pipelines. It is easy to install and use on personal computers and laptops, aiming to bridge the gap between researchers in experimental laboratories and data analysis workflows.
Article
Plant Sciences
Yu-Juan Zhao, Gen-Shen Yin, Xun Gong
Summary: Compared with traditional genetic markers, genomic approaches are valuable for the conservation of endangered species. This study used genome-wide single nucleotide polymorphisms to analyze the genetic diversity and population structure of Paeonia ludlowii, a famous tree peony with rare and pure yellow flowers. The results revealed spatial patterns of genetic variation and suggested that shared ancestry among remnant populations contributes to the subtle population structure. Demographic inference indicated a history of population decline and bottleneck events in P. ludlowii. These findings improve our understanding of the genetic characteristics of this endangered species and have important implications for its conservation.
Article
Biotechnology & Applied Microbiology
Jonathan Foox, Scott W. Tighe, Charles M. Nicolet, Justin M. Zook, Marta Byrska-Bishop, Wayne E. Clarke, Michael M. Khayat, Medhat Mahmoud, Phoebe K. Laaguiby, Zachary T. Herbert, Derek Warner, George S. Grills, Jin Jen, Shawn Levy, Jenny Xiang, Alicia Alonso, Xia Zhao, Wenwei Zhang, Fei Teng, Yonggang Zhao, Haorong Lu, Gary P. Schroth, Giuseppe Narzisi, William Farmerie, Fritz J. Sedlazeck, Don A. Baldwin, Christopher E. Mason
Summary: The study assesses the performance of various massively parallel DNA sequencing platforms on human and bacterial samples, with HiSeq 4000 and X10 performing best among short-read instruments, PacBio CCS leading in long-read instruments, and NovaSeq 6000 being the most effective for capturing insertion/deletion events.
NATURE BIOTECHNOLOGY
(2021)
Article
Evolutionary Biology
Moises A. Bernal, Timothy Ravasi, Giverny G. Rodgers, Philip L. Munday, Jennifer M. Donelson
Summary: This study investigates the effects of temperature exposure on multiple generations of damselfish and finds that the exposure of ancestors and parents to warm conditions can improve the aerobic capacity and gene expression of offspring. Furthermore, the developmental temperature of juveniles has the largest impact on liver gene expression.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Logan Turner, Nathan J. C. Backenstose, Simon Brandl, Moises A. Bernal
Summary: This study reports the first mitochondrial genome for the highfin blenny, Lupinoblennius nicholsi, and reveals a continuous distribution of this species throughout the northern Gulf of Mexico.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Ecology
Katherine M. Eaton, Adam Hallaj, James A. Stoeckel, Moises A. Bernal
Summary: Anthropogenic climate change is leading to more frequent and intense marine heatwaves, which are impacting marine ecosystems. This study focused on the effects of acute warming on pinfish, with results showing that juveniles were more affected metabolically by increased temperatures, particularly in terms of immune function, cell proliferation, muscle contraction, nervous system function, and oxygen transport.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Stanley Kin Nok Chan, Sneha Suresh, Phillip Munday, Timothy Ravasi, Moises A. Bernal, Celia Schunter
Summary: Alternative splicing is a molecular mechanism that allows a gene to encode multiple transcripts and proteins. This study explored the patterns of alternative splicing in the liver of a coral reef fish in response to a marine heatwave. The results showed that acute warming during the onset of the heatwave had a greater impact on alternative splicing than continued exposure to elevated temperatures, and after the heatwave, the fish showed differential splicing of genes related to cyto-protection and post-damage recovery. These findings reveal the role of alternative splicing in the response of coral reef fish to thermal stress.
ECOLOGY AND EVOLUTION
(2022)
Article
Environmental Sciences
Moises A. Bernal, Elliott Schmidt, Jennifer M. Donelson, Philip L. Munday, Timothy Ravasi
Summary: Ocean warming threatens marine biodiversity, but compensatory mechanisms such as plasticity can mitigate the detrimental effects. This study evaluated the transcriptional program of the brain in the coral reef fish Acanthochromis polyacanthus under different warming scenarios. The results showed changes in gene expression related to protein folding, apoptosis, mitochondrial activity, immunity, and circadian regulation.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Moises A. Bernal, Daniel L. Yule, Wendylee Stott, Lori Evrard, Thomas E. Dowling, Trevor J. Krabbenhoft
Summary: Groups of sympatric taxa with low interspecific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This study on the ciscoes in Laurentian Great Lakes used morphometrics, stable isotopes, and transcriptome sequencing to understand the relationships within the Coregonus artedi complex in western Lake Superior. The results showed general concordance for morphological, ecological, and genomic variation, with the genomic data being more taxonomically informative.
Article
Multidisciplinary Sciences
Valeria Ramirez-Castaneda, Erin P. Westeen, Jeffrey Frederick, Sina Amini, Daniel R. Wait, Anang S. Achmadi, Noviar Andayani, Evy Arida, Umilaela Arifin, Moises A. Bernal, Elisa Bonaccorso, Marites Bonachita Sanguila, Rafe M. Brown, Jing Che, F. Peter Condori, Diny Hartiningtias, Anna E. Hiller, Djoko T. Iskandar, Rosa Alicia Jimenez, Rassim Khelifa, Roberto Marquez, Jose G. Martinez-Fonseca, Juan L. Parra, Joshua Penalba, Lina Pinto-Garcia, Onja H. Razafindratsima, Santiago R. Ron, Sara Souza, Jatna Supriatna, Rauri C. K. Bowie, Carla Cicero, Jimmy A. McGuire, Rebecca D. Tarvin
Summary: This article discusses issues of equality, inclusivity, ethics, and safety in field biology research and proposes four guiding principles for equitable practices. It also provides suggestions for global collaborators to make field biology more fair and encourages baseline training.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biodiversity Conservation
Eric D. Crandall, Rachel H. Toczydlowski, Libby Liggins, Ann E. Holmes, Maryam Ghoojaei, Michelle R. Gaither, Briana E. Wham, Andrea L. Pritt, Cory Noble, Tanner J. Anderson, Randi L. Barton, Justin T. Berg, Sofia G. Beskid, Alonso Delgado, Emily Farrell, Nan Himmelsbach, Samantha R. Queeno, Thienthanh Trinh, Courtney Weyand, Andrew Bentley, John Deck, Cynthia Riginos, Gideon S. Bradburd, Robert J. Toonen
Summary: Genetic diversity within species is important for species resilience and conservation policies, but most studies lack the necessary spatial and temporal metadata for reusability and acknowledging sovereignty. We conducted a datathon and found that metadata decayed over time, with successful restoration through papers and online repositories being more effective than contacting authors directly. The rapid decay of metadata availability should prompt updates to data-sharing policies and researcher practices.
CONSERVATION BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hudson T. Pinheiro, Chancey MacDonald, Juan Pablo Quimbayo, Bart Shepherd, Tyler A. Phelps, Ana Carolina Loss, Joao Batista Teixeira, Luiz A. Rocha
Summary: Coral reefs are highly studied ecological assemblages, but the large-scale assembly rules based on empirical quantitative data along the depth gradient have not been investigated. This study reveals that the influence of biogeographic drivers on species richness of coral reef fishes changes significantly with depth, resulting in distinct assemblages governed by different rules in mesophotic coral ecosystems.
Article
Ecology
Brandon Waldo, Katherine Moore, Samuel Bickley, Christopher J. Anderson, Moises A. Bernal
Summary: Environmental conditions play a crucial role in species distribution across ecosystems. This study explored the impact of urbanization on salinity regimes and genetic composition of coastal fishes. The results indicate that urbanization increases salinity variability and promotes genetic structure among killifish populations in the Gulf of Mexico. These findings highlight the significance of understanding the effects of anthropogenic activities on coastal ecosystems.
ENVIRONMENTAL BIOLOGY OF FISHES
(2023)
Editorial Material
Environmental Sciences
Marcelo O. Soares, Pedro H. C. Pereira, Caroline Feitosa, Rodrigo Maggioni, Rafael S. Rocha, Luis Ernesto Arruda Bezerra, Oscar S. Duarte, Sandra Paiva, Eurico Noleto-Filho, Maiara Queiroz M. Silva, Mayra Csapo-Thomaz, Tatiane M. Garcia, Jose Pedro Vieira Arruda Junior, Kelly Ferreira Cottens, Bruno Vinicius, Ricardo Araujo, Clara Buck do Eirado, Lucas Penna Soares Santos, Tainah Correa Seabra Guimaraes, Carlos Henrique Targino, Jose Amorim-Reis Filho, Wagner Cesar Rosa dos Santos, Alex Garcia Cavalleiro de Macedo Klautau, Livio Moreira de Gurjao, Daniel Accioly Nogueira Machado, Rafaela Camargo Maia, Emanuel Soares Santos, Rachel Sabry, Nils Asp, Pedro B. M. Carneiro, Emanuelle F. Rabelo, Tallita C. L. Tavares, Gislaine Vanessa de Lima, Claudio L. S. Sampaio, Luiz A. Rocha, Carlos E. L. Ferreira, Tommaso Giarrizzo
Summary: This article discusses the recently identified invasion of lionfish in Brazil and proposes a roadmap for urgent mitigation, as well as research and management strategies. The invasion in Brazil is already consolidated, with 352 individuals recorded along the coastline, including juveniles, adults, and egg-bearing females. The lionfish invasion in Brazil has covered a wide range of habitats and regions, indicating a rapid and successful invasion process. Concerns are raised regarding the potential ecological impacts on native species that are vulnerable to lionfish predation. An urgent integrated approach with multiple stakeholders, solution-based ecological research, and a national plan are called for to decrease the impact of lionfish invasion. The experience from the Caribbean and Mediterranean invasions will aid in setting and prioritizing goals for Brazil.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Biodiversity Conservation
Juan P. Quimbayo, Rui Freitas, Luiz A. Rocha, Hudson T. Pinheiro
Summary: This study reports the first observation of an adult Guinean angelfish acting as a cleaner for a smaller blackbar soldierfish in the remote Cabo Verde Archipelago, Eastern Atlantic. The cleaning behavior of the angelfish may have a negative effect on the smaller client due to its unique jaw structure.
JOURNAL OF NATURAL HISTORY
(2023)
Article
Multidisciplinary Sciences
Hudson T. Pinheiro, Chancey MacDonald, Robson G. Santos, Ramadhoine Ali, Ayesha Bobat, Benjamin J. Cresswell, Ronaldo Francini-Filho, Rui Freitas, Gemma F. Galbraith, Peter Musembi, Tyler A. Phelps, Juan P. Quimbayo, T. E. Angela L. Quiros, Bart Shepherd, Paris V. Stefanoudis, Sheena Talma, Joao B. Teixeira, Lucy C. Woodall, Luiz A. Rocha
Summary: Coral reefs are being threatened by plastic pollution, in addition to climate change and overfishing. The distribution and quantity of plastics in coral reefs are uncertain, but it has been found that anthropogenic debris, including macroplastics, are present in majority of surveyed reefs. Fishing activities are the main source of plastics in most areas, and macroplastics peak in deeper reefs. These findings can help in designing strategies to address this global threat as the world moves towards a global treaty to tackle plastic pollution.
Article
Biodiversity Conservation
Ricardo S. Rosa, Aline P. M. Medeiros, Antonio Felinto, Camila Brito, Erika F. C. Santana, Fernanda V. Albuquerque, Jonas A. Santos, Julio Lustosa, Katherine M. P. Viana, Marianna B. Silva, Rafael Menezes, Viviana Marquez Velasquez, Alexandre P. Marceniuk, Ronaldo Francini-Filho, Claudia R. Rocha, Luiz A. Rocha, Jesse M. Figueiredo-Filho
Summary: The study compiled the richness of marine teleost fishes from the tropical northeastern Brazilian coast. It presented a systematic list of 571 marine species across 98 families, with 516 species represented by voucher specimens. The study also reported new records, erroneous records, threatened species, and invasive species, providing a baseline for future research in fish systematics, biogeography, ecology, and conservation.
SYSTEMATICS AND BIODIVERSITY
(2023)
Article
Multidisciplinary Sciences
Rodrigo Maggioni, Rafael S. Rocha, Jhonatas T. Viana, Tommaso Giarrizzo, Emanuelle F. Rabelo, Carlos E. L. Ferreira, Claudio L. S. Sampaio, Pedro H. C. Pereira, Luiz A. Rocha, Tallita C. L. Tavares, Marcelo O. Soares
Summary: In 2020, the discovery of lionfish along the Brazilian coastline raised concerns about its potential impact on the coastline and marine protected areas. Genetic analysis showed that these lionfish belong to P. volitans and share genetic similarities with lionfish in the Caribbean Sea. The presence of lionfish in the Amazon mesophotic reefs suggests a possible route of invasion.
SCIENTIFIC REPORTS
(2023)
