Review
Ecology
Marie Tosa, Emily H. Dziedzic, Cara L. Appel, Jenny Urbina, Aimee Massey, Joel Ruprecht, Charlotte E. Eriksson, Jane E. Dolliver, Damon B. Lesmeister, Matthew G. Betts, Carlos A. Peres, Taal Levi
Summary: Ecologists are seeing a renaissance in natural history, now characterized by technological advancements and statistical tools that enable systematic collection and analysis of detailed observations, providing a foundation for hypothetico-deductive research and conservation efforts. Next-generation natural history datasets have transformed anecdotal observations into robust scientific evidence, encouraging scientists to embrace detailed descriptions of nature and engaging both scientists and non-scientists in the wonders of the natural world.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Sihan Zhen, Hongwei Zhang, Yuxin Xie, Song Zhang, Yan Chen, Riliang Gu, Sanzhen Liu, Xuemei Du, Junjie Fu
Summary: PNGSeqR is an R package that provides four BSA algorithms to rapidly define candidate regions and supports DEG and GO analysis, allowing users to choose appropriate analysis methods based on their needs.
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
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Urology & Nephrology
Jose Lazaro-Guevara, Julio Fierro-Morales, A. Hunter Wright, River Gunville, Christopher Simeone, Scott G. Frodsham, Melissa H. Pezzolesi, Courtney A. Zaffino, Laith Al-Rabadi, Nirupama Ramkumar, Marcus G. Pezzolesi
Summary: This study investigated the genetic basis of nondiabetic kidney disease (NDKD) and diabetic kidney disease (DKD) through targeted NGS, finding rare diagnostic variants consistent with clinical diagnoses in 19% of NDKD patients and in 22% of DKD patients. Additionally, genetic variants suggestive of NDKD were detected in 3% of diabetic patients. These findings suggest that rare variants in kidney disease-related genes may contribute to the pathogenesis of DKD and NDKD in patients with diabetes.
AMERICAN JOURNAL OF NEPHROLOGY
(2021)
Article
Clinical Neurology
Jakub Scaber, Alexander G. Thompson, Lucy Farrimond, Emily Feneberg, Malcolm Proudfoot, Lynn Ossher, Martin R. Turner, Kevin Talbot
Summary: This study demonstrates that expanding genetic testing to all patients diagnosed with ALS can enhance recruitment potential for clinical trials, but also has significant resource implications for genetic counseling.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
Article
Physiology
Agnes Bloch-Zupan, Tristan Rey, Alexandra Jimenez-Armijo, Marzena Kawczynski, Naji Kharouf, Muriel de La Dure-Molla, Emmanuelle Noirrit, Magali Hernandez, Clara Joseph-Beaudin, Serena Lopez, Corinne Tardieu, Beatrice Thivichon-Prince, Tatjana Dostalova, Milan Macek Jr, Mustapha El Alloussi, Leila Qebibo, Supawich Morkmued, Patimaporn Pungchanchaikul, Blanca Urzua Orellana, Marie-Cecile Maniere, Benedicte Gerard, Isaac Maximiliano Bugueno, Virginie Laugel-Haushalter
Summary: In this study, next-generation sequencing was used to analyze a cohort of Amelogenesis imperfecta (AI) patients, revealing more than 70 genes associated with AI. The findings showed that 73% of the cases were non-syndromic AI and 27% were syndromic AI. The genetic diagnosis provided important insights for the diagnosis and treatment of AI. This study demonstrated the potential of next-generation sequencing in AI research and provided new insights into the classification and treatment of AI.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Medicine, General & Internal
Shuji Murakami, Tomoyuki Yokose, Daiji Nemoto, Masaki Suzuki, Ryou Usui, Yoshiro Nakahara, Tetsuro Kondo, Terufumi Kato, Haruhiro Saito
Summary: For patients with advanced non-small-cell lung cancer, having a tissue surface area of >= 1 mm^2 is sufficient for successful testing with NGS, regardless of the device used. The success rate of DNA and RNA sequencing was high overall, with large EBUS-GS demonstrating the highest success rates.
Article
Biochemistry & Molecular Biology
Sara-Sophie Poethe, Julia Holtel, Jan-Philip Biermann, Trine Riemer, Melanie Grabmueller, Burkhard Madea, Ralf Thiele, Richard Jaeger
Summary: Forensic DNA profiles are typically established using multiplex PCR amplification and capillary electrophoresis (CE) analysis, but high-throughput next generation sequencing (NGS) techniques have recently been used as an alternative. In this study, an alternative NGS assay called maSTR assay was developed that is cost-effective and performs well in samples with low DNA content, mixed DNA, or PCR inhibitors. The maSTR assay, in conjunction with the SNiPSTR bioinformatics pipeline, is a simple and robust NGS-based STR typing method for human identification in forensic and biomedical contexts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Manasi Majumdar, Cristina Celma, Elaine Pegg, Krunal Polra, Jake Dunning, Javier Martin
Summary: The study focused on a detection method for enteroviruses using NGS analysis of clinical samples, showing high concordance with conventional Sanger sequencing and good sensitivity and specificity for different EV types. The NGS method identified previously untyped EVs and potential co-infections, demonstrating its potential for comprehensive EV detection and genetic analysis.
Article
Medicine, General & Internal
Hestia Mellert, Jordan Reese, Leisa Jackson, Victoria Maxwell, Cherie Tschida, Gary A. Pestano
Summary: Liquid biopsy tests have become crucial in the molecular diagnosis of non-small cell lung cancer patients, with a new method described in this study showing rapid, sensitive, and accurate results through novel amplicon-based targeted next-generation sequencing and high-sensitivity polymerase chain reaction. This method offers a valuable supplement for evaluating targeted mutations from blood, with the potential to conserve specimens while maintaining sensitivity and providing actionable results quickly.
Article
Genetics & Heredity
A. Arizmendi, G. Rudd Garces, J. A. Crespi, L. H. Olivera, L. S. Barrientos, P. Peral Garcia, G. Giovambattista
Summary: This study evaluated the performance of a Canine Targeted Genotyping-by-Sequencing (GBS) custom panel in dog DNA samples, showing its effectiveness in determining parentage and analyzing genetic disorders and traits. However, it was found insufficient in excluding close relatives in inbred populations. The study also identified polymorphic markers and assessed their allele frequencies in the studied breeds, and demonstrated the accuracy of GBS results.
Article
Biochemistry & Molecular Biology
Kang Huang, Wenkai Li, Bing Yang, Dan Wang, Shujun He, Yujia Shen, Jincuo Ao, Yuhang Li, Yunxia Cui, Yuchen Kong, Wei Li, Nianlong Li, Derek W. Dunn, Baoguo Li
Summary: Polyploid plants are important for studying evolution, molecular ecology, and agriculture. However, their unique genetic inheritance requires specific software for population genetic analysis.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Medical Laboratory Technology
Lisa A. Lansdon, Maxime Cadieux-Dion, John C. Herriges, Jeffrey Johnston, Byunggil Yoo, Joseph T. Alaimo, Isabelle Thiffault, Neil Miller, Ana S. A. Cohen, Elena A. Repnikova, Lei Zhang, Midhat S. Farooqi, Emily G. Farrow, Carol J. Saunders
Summary: The study validated the clinical effectiveness of the laboratory's migration from GRCh37 to GRCh38, and identified some important differences between the two genome versions, including discrepancies leading to protein coding sequence variants and discrepancies resolved in coding regions.
CLINICAL CHEMISTRY
(2022)
Article
Urology & Nephrology
Vuthy Ea, Anne Bergougnoux, Pascal Philibert, Nadege Servant-Fauconnet, Alice Faure, Jean Breaud, Laura Gaspari, Charles Sultan, Francoise Paris, Nicolas Kalfa
Summary: The study evaluated the clinical utility of NGS for patients with hypospadias and found that even mild cases can benefit from advanced sequencing techniques. Some variants of unknown significance (VUSs) were identified, but most cases remain unexplained.
Article
Biology
Sean Hoban, Frederick Archer, Laura D. Bertola, Jason G. Bragg, Martin F. Breed, Michael W. Bruford, Melinda A. Coleman, Robert Ekblom, W. Chris Funk, Catherine E. Grueber, Brian K. Hand, Rodolfo Jaffe, Evelyn Jensen, Jeremy S. Johnson, Francine Kershaw, Libby Liggins, Anna J. MacDonald, Joachim Mergeay, Joshua M. Miller, Frank Muller-Karger, David O'Brien, Ivan Paz-Vinas, Kevin M. Potter, Orly Razgour, Cristiano Vernesi, Margaret E. Hunter
Summary: Biodiversity is crucial for the resilience, function, economies, and well-being of ecosystems, but understanding how it sustains ecosystems under stress and environmental change requires new approaches to biodiversity data. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed Essential Biodiversity Variables (EBVs) as fundamental metrics to aggregate and interpret biodiversity observation data. Genetic Composition EBVs (Genetic EBVs), which measure within-species genetic variation, are proposed and ranked according to relevance, sensitivity to change, generalizability, scalability, feasibility, and data availability. The implementation of Genetic EBVs faces challenges in terms of aggregation, standardization, and costs, but advances in genetic data collection and availability provide opportunities for their integration into global conservation policy.
BIOLOGICAL REVIEWS
(2022)
Article
Immunology
Kimberly A. Morrissey, Jordan M. Sampson, Megan Rivera, Lijing Bu, Victoria L. Hansen, Neil J. Gemmell, Michael G. Gardner, Terry Bertozzi, Robert D. Miller
Summary: This study investigated the loss of gamma delta T cells in squamate reptiles and found that it is likely caused by large genomic deletions. The tuatara, a close relative of squamates, was identified as the only squamate reptile that retains gamma delta T cells.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo, Klaus-Peter Koepfli, Lara Urban, Neil J. Gemmell, Heng Li
Summary: This paper presents an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to achieve haplotype-resolved genome assembly from single samples without the need for parent sequencing. The algorithm outperforms existing single-sample assembly pipelines and produces assemblies of similar quality to the best pedigree-based assemblies when applied to human and other vertebrate samples.
NATURE BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Upendra R. Bhattarai, Mandira Katuwal, Robert Poulin, Neil J. Gemmell, Eddy Dowle
Summary: In this study, a high-quality hybrid genome assembly for Forficula auricularia was obtained using Nanopore long-reads and 10x linked-reads. The assembled genome was annotated and analyzed phylogenetically, providing valuable resources for researchers working on dermapterans.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Jean-Francois Doherty, Upendra R. Bhattarai, Sara Ferreira, Robert Poulin, Neil J. Gemmell, Eddy J. Dowle
Summary: Almost every animal trait is strongly associated with parasitic infection or potential exposure to parasites. Accurately determining the status and severity of endoparasitic infection without killing and dissecting the host is a major challenge researchers face. This study demonstrates a noninvasive and minimally stressful method for detecting endoparasitic infection with greater accuracy than dissection alone, improving protocols for live animal studies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Jeunen, Eddy Dowle, Jonika Edgecombe, Ulla von Ammon, Neil J. Gemmell, Hugh Cross
Summary: The measurement of biodiversity plays a vital role in life science research. However, the reliability and accuracy of taxonomic assignment in metabarcoding sequencing data greatly depend on the quality and completeness of reference databases. To address this issue, researchers have developed crabs, a software package that allows the creation of curated reference databases for metabarcoding studies.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Jeunen, Jasmine S. Cane, Sara Ferreira, Francesca Strano, Ulla von Ammon, Hugh Cross, Robert Day, Sean Hesseltine, Kaleb Ellis, Lara Urban, Niall Pearson, Pamela Olmedo-Rojas, Anya Kardailsky, Neil J. Gemmell, Miles Lamare
Summary: Aquatic environmental DNA (eDNA) surveys are revolutionizing marine ecosystem monitoring, but the time-consuming active filtration step remains a bottleneck. This study investigated the similarities and differences between eDNA signals obtained from various sources, including water, filter-feeding organisms, and sponge material. The results showed that vertebrate eDNA signals from water and sponge samples were highly concordant, highlighting the potential of using marine sponges as an additional tool for eDNA-based biodiversity surveys. Caution should be taken to minimize the impact on marine communities during eDNA sampling.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Fisheries
S. Muncaster, A. Goikoetxea, P. M. Lokman, C. E. Moraes, E. L. Damsteegt, J. Edgecombe, N. J. Gemmell, E. V. Todd
Summary: Socially induced sex change is regulated by a combination of genes and epigenetic factors that control sex differentiation and cell fate. The molecular basis for this transformation is still largely unknown. Recent research suggests that both epigenetic effects and genes involved in cell fate are important drivers of sex change.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2023)
Article
Fisheries
Clare I. M. Adams, Gert-Jan Jeunen, Hugh Cross, Helen R. Taylor, Antoine Bagnaro, Kim Currie, Chris Hepburn, Neil J. Gemmell, Lara Urban, Federico Baltar, Michael Stat, Michael Bunce, Michael Knapp
Summary: In response to climate change, efficient monitoring methods are needed for rapidly shifting biodiversity patterns in the oceans. Environmental DNA (eDNA) metabarcoding has emerged as a cost-effective solution. Using eDNA, we detected four community types across a transect in the Southern Hemisphere and found that diversity patterns were mainly driven by planktonic organisms. This technique lays the foundations for multi-trophic environmental monitoring efforts.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Allison K. Miller, Cara L. Brosnahan, Anjali Pande, Cindy F. Baker, Jemma L. Geoghegan, Jane Kitson, Neil J. Gemmell, Edwina J. Dowle
Summary: Infectious diseases have a significant impact on various organisms, and understanding the interactions between hosts and pathogens is crucial for their conservation and management. The use of genomic approaches has made it easier to obtain this knowledge quickly, however, many species still face challenges in accessing appropriate samples and data. Archival materials, such as formalin-fixed paraffin-embedded tissue samples, may provide a valuable resource for studying pathogen emergence and host responses over long periods of time.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Zoology
Kaj Kamstra, Chloe van der Burg, Haylee M. Quertermous, Simon Muncaster, Erica V. Todd, Christine L. Jasoni, Culum Brown, Neil J. Gemmell
Summary: For most vertebrates, sexual fate is genetically determined and remains fixed throughout life. However, for some teleost fishes sex is more plastic. Significant progress has been made in characterising the cellular and molecular processes that underpin gonadal sex change. The brain-mediated mechanisms that underlie and initiate this transformation, however, remain poorly understood.
NEW ZEALAND JOURNAL OF ZOOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andrew T. M. Bagshaw, Neil J. Gemmell
Summary: In recent years, scientists have shifted their focus from studying the relationships between adjacent nucleotides to exploring the larger scale structure of DNA. A little-known technique called non-denaturing bisulfite modification of genomic DNA in conjunction with high-throughput sequencing has provided valuable insights. This technique has revealed a gradient in reactivity that increases towards the 5' end of poly-dC:dG mononucleotide repeats, suggesting the presence of positive-roll bending not predicted by existing models. Furthermore, these repeats are enriched at positions relative to the nucleosome dyad that bend towards the major groove, providing important information about DNA packaging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Nataliya Timoshevskaya, Kaan Eskut, Vladimir A. Timoshevskiy, Sofia M. C. Robb, Carson Holt, Jon E. Hess, Hugo J. Parker, Cindy F. Baker, Allison K. Miller, Cody Saraceno, Mark Yandell, Robb Krumlauf, Shawn R. Narum, Ralph T. Lampman, Neil J. Gemmell, Jacquelyn Mountcastle, Bettina Haase, Jennifer R. Balacco, Giulio Formenti, Sarah Pelan, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D. Jarvis, Jeramiah J. Smith
Summary: Programmed DNA loss is a gene silencing mechanism found in various vertebrate and nonvertebrate lineages. The evolution of somatically eliminated sequences in these species has been difficult to reconstruct due to repetitive and duplicated sequences. However, an improved assembly of the sea lamprey genome has enabled analysis that sheds light on the recruitment of genes to the germline-specific fraction and reveals the roles of segmental duplication and positive selection in the long-term evolution of germline-specific chromosomes.
Meeting Abstract
Zoology
K. A. Morrissey, J. Samson, M. Rivera, L. Bu, V. L. Hansen, N. J. Gemmell, M. G. Gardner, T. Bertozzi, R. D. Miller
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anna C. Clark, Rey Edison, Kevin Esvelt, Sebastian Kamau, Ludovic Dutoit, Jackson Champer, Samuel E. Champer, Philipp W. Messer, Alana Alexander, Neil J. Gemmell
Summary: This manuscript introduces a framework for identifying and evaluating target genes based on biological gene function, gene expression, and results from mouse knockout models. The framework identifies 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other genetic pest control technologies.
MOLECULAR ECOLOGY RESOURCES
(2023)
