Article
Fisheries
Ane del Rio Lavin, Natalia Diaz-Arce, Maria Angelica Larrain, Cristian Araneda, Naiara Rodriguez-Ezpeleta, Elisa Jimenez, Miguel Angel Pardo
Summary: Seafood traceability is important for regulators and fishing industries to prevent fraud and ensure consumer safety. This study used genetic markers to trace the genetic structure of Mediterranean mussel and assess the ability of new markers to trace the origin of samples. The results showed clear differentiation between populations from different regions and suggested the potential for developing an accurate and cost-effective traceability tool.
Article
Plant Sciences
Sajad U. Nabi, Virendra K. Baranwal, Govind P. Rao, Sheikh Mansoor, Carmen Vladulescu, Wasim H. Raja, Basit L. Jan, Saleh Alansi
Summary: Through RNA sequencing of symptomatic and asymptomatic apple plants, this study identified five viruses and one viroid associated with apple mosaic disease. The complete genomes of these viruses and viroid were reconstructed, revealing genetic diversity and recombination events.
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)
Article
Biodiversity Conservation
Fabienne Van Rossum, Sarah Le Pajolec, Cecile Gode
Summary: Plant translocations are a solution for rescuing nonviable populations and recreating population networks. Genetic diversity enhancement or maintenance in post-translocation generations is essential for translocation success. Spatial patterns of genetic diversity in the first post-translocation generation of translocated populations were investigated in this study. The results showed that the genetic diversity in the first post-translocation generation is representative of the natural seed-source populations, and the mixed spatial arrangement of transplants contributed to enhanced genetic diversity, random mating, and high admixture levels. Stronger spatial genetic structure might impact long-term population genetic sustainability.
GLOBAL ECOLOGY AND CONSERVATION
(2023)
Article
Food Science & Technology
Lijin Duan, Shasha Zhang, Yingxia Yang, Qian Wang, Qingkuo Lan, Yong Wang, Wentao Xu, Wujun Jin, Liang Li, Rui Chen
Summary: This study introduces a novel GMO testing method, "SSH-seq", based on suppressive subtractive hybridization and next-generation sequencing, which can be used to detect unknown GMOs and has shown promising results in experiments. Although the method may be influenced by multiple factors, further optimizations could make SSH-seq a powerful tool in the field of GMO testing.
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.
Review
Biochemistry & Molecular Biology
Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati, Bruna Scaggiante
Summary: The poor survival of triple-negative breast cancer (TNBC) is attributed to its aggressive behavior, large heterogeneity, and high risk of recurrence. Next-generation sequencing (NGS) has been used to investigate the molecular characteristics of TNBC, revealing recurrent pathogenic alterations in TP53, immunocheckpoint response genes, and PIK3CA and DNA repair pathways. NGS has also identified potential personalized treatments and novel biomarkers such as AURKA, MYC, and JARID2 mutations. Additionally, NGS studies have identified ethnicity-specific alterations in African and African American TNBC, including EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation. The development of long-read sequencing methods and their combination with optimized short-read techniques hold promise for improving the efficiency of NGS approaches in future clinical use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Isaac Miller-Crews, Mikhail Matz, Hans A. Hofmann
Summary: Next-generation sequencing technology has transformed genotyping in various fields, but parentage analysis still often relies on costly microsatellite markers. 2b-RAD sequencing offers a cost-effective and efficient alternative for parentage analysis, enabling inference of familial relationships from mixed DNA samples and populations. Our novel genetic testing pipeline, utilizing 2b-RAD, overcomes obstacles faced by other methods and allows straightforward and cost-effective parentage analysis in any species.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Lin Wang, Jixuan Yang, Hong Zhang, Qin Tao, Yuxin Zhang, Zhenyu Dang, Fengjun Zhang, Zewei Luo
Summary: Polyploidy plays a crucial role in plant evolution, but genotyping by sequencing (GBS) presents different challenges in diploid and polyploid species. This paper introduces statistical methods for predicting the sequence reads required for accurate GBS in polyploids and validates the theoretical predictions using RAD-seq data from tetraploid potato cultivars.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Chemistry, Multidisciplinary
Vasilka Chopkova, Mariana Petkova, Stefan Shilev
Summary: This study investigated the bacterial diversity of mesophilic and thermophilic phases of composting in two different sites using Illumina HiSeq sequencing and phylogenetic analysis. The results showed that the mesophilic phase had a higher number of bacterial species compared to the thermophilic phase, and there were differences in bacterial diversity between the two composting sites.
APPLIED SCIENCES-BASEL
(2023)
Article
Environmental Sciences
Sine Alise Hartvigsen Hansen, Sigmund Ramberg, Nadezhda Lekanova, Bjorn Hoyheim, Tor Einar Horsberg, Rune Andreassen, Marit Jorgensen Bakke
Summary: In this study, a full-length transcriptome of the ectoparasitic salmon louse was generated using a combination of long-read and short-read sequencing. A total of 31,092 high-accuracy full-length transcripts were identified, with over half being specific to either the copepodid or adult life stage. This resource can be applied in expression studies, SNP mining, and exploring gene networks and enrichment analysis following expression studies.
FRONTIERS IN MARINE SCIENCE
(2023)
Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Article
Pharmacology & Pharmacy
Shuangyu Han, Zhan Zhao, Lei Yang, Jie Huang, Yubao Wang, Jing Feng
Summary: mNGS has become increasingly popular for detecting infectious organisms. This study compared the performance of Illumina and BGI platforms in detecting pulmonary pathogens, and found that both platforms had similar diagnostic performance and were superior to conventional examinations.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Forestry
Atsushi Ejima, Kentaro Uchiyama, Hideki Mori, Yoshihiko Tsumura
Summary: This study tested the use of genomic prediction (GP) to improve the efficiency of breeding long-lived trees, specifically Cryptomeria japonica. The results showed that GP was more accurate than traditional pedigree-based methods, but parent-offspring relationships reduced its accuracy for traits strongly affected by selection pressure.
Article
Evolutionary Biology
Andrew P. Anderson, Emily Rose, Sarah P. Flanagan, Adam G. Jones
JOURNAL OF HEREDITY
(2020)
Article
Ecology
Brian A. Lerch, Kimberly A. Dautel, Sharee Brewer, Alan Liang, Nourridine Siewe, Sarah Flanagan
POPULATION ECOLOGY
(2020)
Article
Ecology
Jonathan M. Henshaw, Michael B. Morrissey, Adam G. Jones
Article
Behavioral Sciences
Bernadette D. Johnson, Avrie Fox, Landon R. Wright, Ginger E. Carney, Barrie D. Robison, Adam G. Jones
Summary: The African turquoise killifish is the shortest-lived vertebrate research model, suitable for studying sexual selection. Females of this species prefer animated males with specific tail colors, indicating potential for studying genetic basis of preferences and reproductive behaviors. N. furzeri represents an untapped model with stable and repeatable female responses to male animations, making it a promising research tool.
Article
Biochemistry & Molecular Biology
Sarah P. Flanagan, Emily Rose, Adam G. Jones
Summary: The study shows that colonization of freshwater habitats by the Gulf pipefish involves similar genomic regions across different geographical distances and environmental conditions. These similar patterns are likely facilitated by the interacting effects of intrinsic barriers, gene flow among populations, and ecological selection.
Article
Behavioral Sciences
Charlotta Kvarnemo, Susanne E. Andersson, Jonas Elisson, Glenn Moore, Adam G. Jones
Summary: Genetic monogamy is common in seahorse species like the West Australian seahorse Hippocampus subelongatus. Females have larger home ranges and move greater distances compared to males. Paired individuals have more overlap in home ranges than unpaired individuals.
JOURNAL OF ETHOLOGY
(2021)
Review
Zoology
Lucy Howell, Michelle LaRue, Sarah P. Flanagan
Summary: This paper evaluates the potential of using environmental DNA methods for biodiversity monitoring and conservation genetics research in Antarctica. Most Antarctic eDNA studies have focused on microbial metabarcoding, with limited research on vertebrates, but some creative examples have effectively used eDNA for studying vertebrates. Portable sequencing technologies have the potential to shape the future of eDNA research in Antarctica, which could be a valuable tool for assessing, monitoring, and conserving biodiversity in the region.
NEW ZEALAND JOURNAL OF ZOOLOGY
(2021)
Review
Ecology
Erik Svensson, Stevan J. Arnold, Reinhard Buerger, Katalin Csillery, Jeremy Draghi, Jonathan M. Henshaw, Adam G. Jones, Stephen De Lisle, David A. Marques, Katrina McGuigan, Monique N. Simon, Anna Runemark
Summary: Correlational selection operates on combinations of traits, impacting genomic architecture and evolution across various fields. Integrating evolutionary research in different fields through a genomics lens is key in understanding how correlational selection shapes genetic diversity.
NATURE ECOLOGY & EVOLUTION
(2021)
Review
Evolutionary Biology
Karoline Fritzsche, Jonathan M. Henshaw, Bernadette D. Johnson, Adam G. Jones
Summary: The 150th anniversary of Charles Darwin's book "The Descent of Man" is marked in 2021, highlighting the insight that in some species, females compete for mates. These sex-role-reversed species have challenged preconceptions and enriched the understanding of animal mating systems. They continue to hold untapped potential for future research on sexual selection.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Ecology
Andrew P. Anderson, Adam G. Jones
Summary: Sexual selection has driven the evolution of sexually dimorphic traits in male vertebrates, which are controlled by androgen signaling involving androgen response elements (AREs). Changes in the number and genomic locations of AREs can affect gene expression and receptor regulation. By analyzing primate genomes, we found that sexual selection strength is related to the genome-wide number of AREs, and changes in AREs are correlated with changes in male expression levels and sex-biased gene expression.
Article
Environmental Sciences
Micaela Pullen, Derek Gerber, Mads Solgaard Thomsen, Sarah P. Flanagan
Summary: Biodiversity is crucial for communities to adapt to changes, and its patterns naturally fluctuate over time. This study investigated the impacts of seasonality, seagrass cover changes, and spatial location on a temperate seagrass bed in New Zealand. The study found that season, seagrass cover, and location explained 88.5% of the variation in community composition. Species abundances and composition changed over seasons.
ESTUARIES AND COASTS
(2022)
Article
Ecology
Bernadette D. Johnson, Andrew P. Anderson, Clayton M. Small, Emily Rose, Sarah P. Flanagan, Corey Hendrickson-Rose, Adam G. Jones
Summary: Male pregnant pipefishes have evolved differently in terms of the evolution and expression of testis-related genes compared to other fish, indicating the absence of strong selection pressure. They have lost important classes of genes from their testis transcriptomes.
Review
Ecology
Nicole M. Tosto, Emily R. Beasley, Bob B. M. Wong, Judith E. Mank, Sarah P. Flanagan
Summary: This Review discusses the impact of sexual selection and sexual conflict on genomes and transcriptomes and proposes an integrative approach to understand these processes. Sexual dimorphism, resulting from shared genomic variation, is a common example of phenotypic variation within species. Gene expression differences between sexes contribute to sexual dimorphisms. However, distinguishing the role of sexual selection in the evolution of sexually dimorphic gene expression remains challenging. The proposed framework suggests a comparative approach that incorporates molecular mechanisms and is expected to provide valuable insights in various fields.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Fleur van Eyndhoven, Elissa Z. Cameron, Sarah P. Flanagan
Summary: This study reports courtship displays in the wide-bodied pipefish, a species with extreme sexual dimorphism. Surprisingly, females also use their sex-specific ornament during courtship, while males initiate chasing behaviors in some cases. These findings provide important insights into the potential roles of sexual selection and sexual conflict in shaping sexual dimorphism.
ROYAL SOCIETY OPEN SCIENCE
(2023)