Article
Environmental Sciences
Sarrah M. Dunham-Cheatham, Kelly B. Klingler, Margarita Vargas Estrada, Mae Sexauer Gustin
Summary: Studies have found high concentrations of mercury in some commercial pet food products, with limited research on methylmercury. Three tested pet food products exceeded suggested mercury limits, but methylmercury levels were safe. Genetic tools were used to analyze ingredients, revealing consistency and adulteration in pet food products.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Yawen Mu, Chao Song, Jianghua Yang, Yong Zhang, Xiaowei Zhang
Summary: This study used DNA barcoding to identify species and assess biodiversity of fish in Tai Lake. High-throughput sequencing greatly improved the capture rate of barcode sequences of fish, and barcode gap analysis successfully delineated species in all specimens. The results are expected to provide new insights into fish diversity conservation in Tai Lake.
Review
Fisheries
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat
Summary: The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.
AQUACULTURE RESEARCH
(2021)
Review
Engineering, Marine
Cora Hoerstmann, Sylke Wohlrab, Uwe John
Summary: High-throughput sequencing technologies have advanced our understanding of microbial diversity in the oceans, but research on microbial eukaryotes (protists) lags behind. This review discusses the challenges and opportunities of high-throughput sequencing methods for studying the evolutionary, ecological, and functional aspects of oceanic protists. These approaches allow for a deeper understanding of the functional role of protists and the changes in marine ecosystems.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Environmental Sciences
Conny P. Serite, Arsalan Emami-Khoyi, Ofentse K. Ntshudisane, Nicola C. James, Bettine Jansen van Vuuren, Taryn Bodill, Paul D. Cowley, Alan K. Whitfield, Peter R. Teske
Summary: Understanding the dietary preferences of endangered species is important for conservation strategies. The study compared metabarcoding and metagenomics to analyze the diets of endangered pipefish species. Metabarcoding showed a difference in prey preference between the two species, while metagenomics identified additional copepod species in one species' diet. Metagenomics was found to be a useful complementary method for dietary analysis, although it is more affected by a lack of reference sequences.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Le Zhang, Yi-Wei Huang, Jia-Lin Huang, Ji-Dong Ya, Meng-Qing Zhe, Chun-Xia Zeng, Zhi-Rong Zhang, Shi-Bao Zhang, De-Zhu Li, Hong-Tao Li, Jun-Bo Yang
Summary: In this study, DNA barcoding was conducted for species identification of Cymbidium using plastomes. A comprehensive DNA barcode reference library for Cymbidium species identification was established. The plastome showed improved species identification rates compared to standard DNA barcodes, but still had limitations. Nuclear genome data were also explored for species identification and showed potential as next-generation nuclear barcodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Engineering, Environmental
Emily Garner, Benjamin C. Davis, Erin Milligan, Matthew Forrest Blair, Ishi Keenum, Ayella Maile-Moskowitz, Jin Pan, Mariah Gnegy, Krista Liguori, Suraj Gupta, Aaron J. Prussin, Linsey C. Marr, Lenwood S. Heath, Peter J. Vikesland, Liqing Zhang, Amy Pruden
Summary: The emergence of NGS technologies has revolutionized the water industry's ability to address complex microbiological challenges, although faced with barriers like cost and expertise. Research has focused on the applications of NGS in water, wastewater, and recycled water, highlighting key contributions and future directions for advancement.
Review
Microbiology
Maria Aragona, Anita Haegi, Maria Teresa Valente, Luca Riccioni, Laura Orzali, Salvatore Vitale, Laura Luongo, Alessandro Infantino
Summary: The fast and affordable high-throughput sequencing has led to new developments in plant pathology, including phylogenomics and genome comparison in fungal taxonomy, as well as the application of metabarcoding and metagenomics techniques in analyzing complex diseases and environmental interactions. These technologies generate big data that require sophisticated bioinformatic tools for management.
Article
Multidisciplinary Sciences
Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li
Summary: This review summarizes the potential applications and challenges of metagenomic next-generation sequencing (mNGS) in the diagnosis of lower respiratory tract infections (LRIs), aiming to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Duong Vu, R. Henrik Nilsson, Gerard J. M. Verkley
Summary: A new tool, dnabarcoder, was introduced to optimize the accuracy and precision of fungal molecular identification and classification by predicting local similarity cutoffs for different clades of fungi. Extracting the ITS region from the ITS DNA barcode data set significantly improved accuracy and precision, and varying similarity cutoffs were observed between different clades.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Ecology
Karen L. Bell, Robert A. Petit, Anya Cutler, Emily K. Dobbs, J. Michael Macpherson, Timothy D. Read, Kevin S. Burgess, Berry J. Brosi
Summary: In this study, the performance of whole-genome shotgun (WGS) sequencing for species identification and quantitative analysis of pollen was evaluated. WGS showed near 100% accuracy in species identification in mixtures but generated higher rates of false positives compared to rbcL and ITS2 amplicon sequencing. WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion for relative species abundance quantification, but diverged more from a 1:1 relationship.
ECOLOGY AND EVOLUTION
(2021)
Article
Medicine, Legal
Shubham Yadav, Vijay Tripathi, Vaibhav Saran
Summary: Characterization of human saliva through Next-Generation Sequencing has revealed the influence of habits, such as smoking, alcohol consumption, and vegan diet, on the microbial composition and diversity of the salivary microbiome.
FORENSIC SCIENCE INTERNATIONAL
(2023)
Article
Microbiology
Andrew N. Miller, Jason Karakehian, Daniel B. Raudabaugh
Summary: Fungaria is an important resource for genetic data, especially for type specimens. However, ancient specimens often have fragmented and contaminated DNA, making sequencing difficult. This study successfully extracted and sequenced DNA from recent and ancient specimens, generating correct sequences for five samples. The results contribute to ongoing systematic studies.
Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Ravina Kullar, Emanuele Chisari, James Snyder, Christopher Cooper, Javad Parvizi, Jason Sniffen
Summary: This article discusses the gaps in traditional culture and introduces the utility of next-generation sequencing (NGS) in diagnosing and treating peri-prosthetic joint infections. It highlights the clinical benefits of using NGS compared to culture alone and emphasizes the potential of NGS in improving the yield of identifying infective organisms in challenging cases.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Ecology
Tristan Cumer, Francois Pompanon, Frederic Boyer
Article
Biochemistry & Molecular Biology
Hsin Lee, Wei-Jen Chen, Nicolas Puillandre, Laetitia Aznar-Cormano, Mong-Hsun Tsai, Sarah Samadi
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2019)
Article
Multidisciplinary Sciences
Juliette Delavenne, Louise Keszler, Magalie Castelin, Pierre Lozouet, Philippe Maestrati, Sarah Sarnadi
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
Ibrahim Belabdi, Abdessamad Ouhrouch, Mohamed Lafri, Semir Bechir Suheil Gaouar, Elena Ciani, Ahmed Redha Benali, Hakim Ould Ouelhadj, Abdelmajid Haddioui, Francois Pompanon, Veronique Blanquet, Dominique Taurisson-Mouret, Sahraoui Harkat, Johannes A. Lenstra, Badr Benjelloun, Anne Da Silva
SCIENTIFIC REPORTS
(2019)
Article
Evolutionary Biology
Tristan Cumer, Frederic Boyer, Francois Pompanon
Summary: The study investigated the role of structural variations (SVs) during domestication and improvement of small ruminants by analyzing whole-genome sequences of domestic sheep, goats, and their wild relatives. The research identified numerous SVs related to physiological traits, reproduction, and immunity, which showed significant differences between wild and domestic species. These SVs, which would not have been detected through SNP screening alone, demonstrate the complementary nature of SVs and SNP-based approaches in detecting selection signatures.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Adeline Stewart, Delphine Rioux, Frederic Boyer, Ludovic Gielly, Francois Pompanon, Amelie Saillard, Wilfried Thuiller, Jean-Gabriel Valay, Eric Marechal, Eric Coissac
Summary: The study found that the distribution of green algae in the Alps is influenced by altitude, based on analysis of soil samples collected from different depths in the French Alps. Elevation was shown to be a strong correlate of species and genus level distribution of green algae in the region.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Bruno Serranito, Dominique Taurisson-Mouret, Sahraoui Harkat, Abbas Laoun, Nadjet-Amina Ouchene-Khelifi, Francois Pompanon, Badr Benjelloun, Giuliano Cecchi, Sophie Thevenon, Johannes A. Lenstra, Anne Da Silva
Summary: This study analyzed two datasets of goats from West-Central Africa and East Africa using LFMM and PCAdapt to identify molecular signatures related to trypanotolerance. The most plausible signatures of trypanotolerance point to specific genes. The study highlights the importance of protecting local breeds.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Bruno Serranito, Marco Cavalazzi, Pablo Vidal, Dominique Taurisson-Mouret, Elena Ciani, Marie Bal, Eric Rouvellac, Bertrand Servin, Carole Moreno-Romieux, Gwenola Tosser-Klopp, Stephen J. G. Hall, Johannes A. Lenstra, Francois Pompanon, Badr Benjelloun, Anne Da Silva
Summary: This study focused on local Mediterranean breeds of goats and sheep, using historical archives and statistical programs to identify adaptive genes, revealing their potential key roles in arid and altitude gradients.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Abdessamad Ouhrouch, Simon Boitard, Frederic Boyer, Bertrand Servin, Anne Da Silva, Francois Pompanon, Abdelmajid Haddioui, Badr Benjelloun
Summary: Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. The study revealed that Moroccan local sheep breeds exhibit high genetic diversity and a large set of adaptive variations, making them a valuable genetic resource for the conservation of sheep in the context of climate change.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Laure Denoyelle, Pierre de Villemereuil, Frederic Boyer, Meidhi Khelifi, Clement Gaffet, Florian Alberto, Badr Benjelloun, Francois Pompanon
Summary: The study investigated genetic and epigenetic variations in sheep and goats from Morocco, identifying candidate genes related to environmental perception, immunity, reproduction, and production. Additionally, differentially methylated genes associated with milk production and muscle development were found in both species. The comparison of genomic regions affected by genetic and epigenetic variations revealed that climatic variations impacted similar biological pathways but different genes in sheep and goats.
FRONTIERS IN GENETICS
(2021)
Article
Environmental Sciences
Melissa Hanafi-Portier, Sarah Samadi, Laure Corbari, Tin-Yam Chan, Wei-Jen Chen, Jhen-Nien Chen, Mao-Ying Lee, Christopher Mah, Thomas Saucede, Catherine Borremans, Karine Olu
Summary: Imagery has become an important tool for assessing deep-sea biodiversity, providing quantitative and repeatable estimates. Taxon identification from images is challenging, especially in regions where faunal knowledge is limited. The efficiency of imagery and physical sampling may vary among different habitat types.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Charlotte Her, Hamid-Reza Rezaei, Sandrine Hughes, Saeid Naderi, Marilyne Duffraisse, Marjan Mashkour, Hamid-Reza Naghash, Adrian Balasescu, Gordon Luikart, Steve Jordan, Deniz Ozut, Aykut Kence, Michael W. Bruford, Anne Tresset, Jean-Denis Vigne, Pierre Taberlet, Catherine Hanni, Francois Pompanon
Summary: This study investigated the controversial origin of domestic sheep, confirming that the Asiatic mouflon is the maternal ancestor of sheep and identifying the domestication center in eastern Anatolia and central Zagros. The study also found multiple mitochondrial haplogroups in the domestication process.
Article
Zoology
Hsin Lee, Nicolas Puillandre, Yasunori Kano, Wei-Jen Chen, Sarah Samadi
Summary: This study investigates the species diversity of the family Cocculinidae using an integrated approach. The results reveal high diversity in the Indo-West Pacific region, with many species not assigned to known names. Additionally, a previously unknown copulatory structure and ten main clades in the family were discovered.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Agriculture, Dairy & Animal Science
Laure Denoyelle, Estelle Talouarn, Philippe Bardou, Licia Colli, Adriana Alberti, Coralie Danchin, Marcello Del Corvo, Stefan Engelen, Celine Orvain, Isabelle Palhiere, Rachel Rupp, Julien Sarry, Mazdak Salavati, Marcel Amills, Emily Clark, Paola Crepaldi, Thomas Faraut, Clet Wandui Masiga, Francois Pompanon, Benjamin D. Rosen, Alessandra Stella, Curtis P. Van Tassell, Gwenola Tosser-Klopp
Summary: The VarGoats project aimed to understand the genetic diversity of domestic goats through an international 1000-genome resequencing program. The dataset collected included sequenced goats from various regions and identified numerous genetic variations. The study found that goat populations from different continents tend to cluster into independent groups, reflecting their diverse genetic backgrounds and geographic origins.
GENETICS SELECTION EVOLUTION
(2021)
Article
Anthropology
Emmanuelle Vila, Philippe Abrahami, Moussab Albesso, Agraw Amane, Camille Bader, Remi Berthon, Sofiane Bouzid, Daniel Bradley, Catherine Breniquet, Jwana Chahoud, Thomas Cucchi, Hossein Davoudi, Bea de Cupere, Gilles Escarguel, Oscar Estrada, Lionel Gourichon, Daniel Helmer, Wei Huangfu, Josephine Lesur, Marjan Mashkour, Cecile Michel, Azadeh Mohaseb, Ludovic Orlando, Francois Pompanon, Jacqueline Studer, Manon Vuillien
Summary: The EVOSHEEP project uses a combination of archaeozoology, geometric morphometrics, and genetics to study changes in the physical appearance and phenotypic characteristics of archaeological sheep assemblages in various regions, and how these changes are related to the appearance of new breeds and the demand for secondary products in the textile industry.
