Shashank, Pathour R Parker, Brandon M Rananaware, Santosh R Plotkin, David Couch, Christian Yang, Lilia G Nguyen, Long T Prasannakumar, N R Braswell, W Evan Jain, Piyush K
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Published in
Molecular ecology resources
Rapid identification of organisms is essential for many biological and medical disciplines, from understanding basic ecosystem processes, disease diagnosis, to the detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high...
Wu, Luhan Osugi, Tomonori Inagawa, Takashi Okitsu, Jiro Sakamoto, Shogo Minamoto, Toshifumi
Published in
Molecular ecology resources
Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, t...
Kestel, Joshua H Bateman, Philip W Field, David L White, Nicole E Lines, Rose Nevill, Paul
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Molecular ecology resources
In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive,...
Xie, Tingting Orr, Michael C Zhang, Dan Ferrari, Rafael R Li, Yi Liu, Xiuwei Niu, Zeqing Wang, Mingqiang Zhou, Qingsong Hao, Jiasheng
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Published in
Molecular ecology resources
The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA...
Chapuis, Marie-Pierre Benoit, Laure Galan, Maxime
Published in
Molecular ecology resources
Gaining meaningful insights into bacterial communities associated with animal hosts requires the provision of high-quality nucleic acids. Although many studies have compared DNA extraction methods for samples with low bacterial biomass (e.g. water) or specific PCR inhibitors (e.g. plants), DNA extraction bias in samples without inherent technical c...
Laine, Veronika N Sepers, Bernice Lindner, Melanie Gawehns, Fleur Ruuskanen, Suvi van Oers, Kees
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Molecular ecology resources
The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally developed for research on humans and model species are now regularly used in ecological and evolutionary research. There is also a growing interest in the causes and con...
Gu, Jingjing Li, Sheng Zhu, Bo Liang, Qiqi Chen, Bin Tang, Xiangwei Chen, Chujie Wu, Dong-Dong Li, Yan
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Molecular ecology resources
Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed hor...
Hakimzadeh, Ali Abdala Asbun, Alejandro Albanese, Davide Bernard, Maria Buchner, Dominik Callahan, Benjamin Caporaso, J Gregory Curd, Emily Djemiel, Christophe Brandström Durling, Mikael
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Published in
Molecular ecology resources
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers h...
Lentendu, Guillaume Bruni, Estelle P Ah-Peng, Claudine Fujinuma, Junichi Kubota, Yasuhiro Lorite, Juan Peñas, Julio Huang, Shuyin Strasberg, Dominique Vittoz, Pascal
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Published in
Molecular ecology resources
A large part of the soil protist diversity is missed in metabarcoding studies based on 0.25 g of soil environmental DNA (eDNA) and universal primers due to ca. 80% co-amplification of non-target plants, animals and fungi. To overcome this problem, enrichment of the substrate used for eDNA extraction is an easily implemented option but its effect ha...
Gendron, Eli M Sevigny, Joseph L Byiringiro, Innocent Thomas, W Kelley Powers, Thomas O Porazinska, Dorota L
Published in
Molecular ecology resources
DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to i...