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An Innovative Binding-Protein-Based dsRNA Extraction Method: Comparison of Cost-Effectiveness of Virus Detection Methods Using High-Throughput Sequencing. 一种创新的基于结合蛋白的dsRNA提取方法:使用高通量测序的病毒检测方法的成本效益比较。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-05-15 DOI: 10.1111/1755-0998.14111
Mamadou L Fall, Dong Xu, Pierre Lemoyne, Geneviève Clément, Peter Moffett, Christophe Ritzenthaler
{"title":"An Innovative Binding-Protein-Based dsRNA Extraction Method: Comparison of Cost-Effectiveness of Virus Detection Methods Using High-Throughput Sequencing.","authors":"Mamadou L Fall, Dong Xu, Pierre Lemoyne, Geneviève Clément, Peter Moffett, Christophe Ritzenthaler","doi":"10.1111/1755-0998.14111","DOIUrl":"https://doi.org/10.1111/1755-0998.14111","url":null,"abstract":"<p><p>Viral diseases represent a threat to global food production. Managing the impact of viruses on crop production requires the ability to monitor viruses, study their ecology and anticipate outbreaks. Double-stranded RNA (dsRNA) sequencing is a well-established and reliable method of detecting viruses and studying virome-host interactions and ecology. Compared to total RNA extraction, dsRNA extraction eliminates the majority of host RNAs, improving the recovery of viral RNAs. In this study, we developed and evaluated a novel dsRNA extraction method for high-throughput sequencing (HTS) applications based on the Flock House virus (FHV) B2 protein (B2-based method), and compared its performance with that of established cellulose-based and DRB4-based methods (commercial kit), as well as total RNA extraction techniques. The electrostatic properties of B2 have been instrumental in developing a bead-free and resin-free dsRNA extraction method. The B2-based method demonstrated high viral read recovery, achieving proportions exceeding 20% in most samples, and provided better dsRNA purity with less low weight molecule co-extracted RNA than the DRB4-based method and cellulose-based methods. Despite producing overall fewer total reads than the DRB4-based method, the B2-based enrichment for viral-derived dsRNA was better, with a higher percentage of viral reads, making it effective in virome profiling. Furthermore, it had an excellent detection specificity (0.97) and a good detection sensitivity (0.71), minimising false positives and false negatives. In addition, the B2-based method proved to be highly cost-effective, with a per-reaction cost of $4.47, compared to $35.34 for the DRB4-based method. This method offers a practical solution for laboratories with limited resources or for large-scale sampling for viral ecology studies. Future improvements to the B2-based method should focus on optimising sensitivity to Vitivirus species and developing scalable, automated workflows for high-throughput viral detection.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14111"},"PeriodicalIF":5.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Observation Bias in Metabarcoding. 元条形码中的观察偏差。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-05-15 DOI: 10.1111/1755-0998.14119
Megan R Shaffer, Elizabeth Andruszkiewicz Allan, Amy M Van Cise, Kim M Parsons, Andrew Olaf Shelton, Ryan P Kelly
{"title":"Observation Bias in Metabarcoding.","authors":"Megan R Shaffer, Elizabeth Andruszkiewicz Allan, Amy M Van Cise, Kim M Parsons, Andrew Olaf Shelton, Ryan P Kelly","doi":"10.1111/1755-0998.14119","DOIUrl":"https://doi.org/10.1111/1755-0998.14119","url":null,"abstract":"<p><p>DNA metabarcoding is subject to observation bias associated with PCR and sequencing, which can result in observed read proportions differing from actual species proportions in the DNA extract. Here, we amplify and sequence a mock community of known composition containing marine fishes and cetaceans using four different primer sets and a variety of PCR conditions. We first compare metabarcoding observations to two different sets of expected species proportions based on total genomic DNA and on target mitochondrial template DNA. We find that calibrating observed read proportions based on template DNA concentration is most appropriate as it isolates PCR amplification bias; calibration with total genomic DNA results in bias that can be attributed to both PCR amplification bias and differing ratios of template to total genomic DNA. We then model the remaining amplification bias and find that approximately 60% can be explained by inherent species-specific DNA characteristics. These include primer-template mismatches, amplicon fragment length, and GC content, which vary somewhat across Taq polymerases. Finally, we investigate how different PCR protocols influence community composition regardless of expected proportions and find that changing protocols most strongly influence the amplification of templates with primer mismatches. Our findings suggest that using primer-template pairs without mismatches and targeting a narrow taxonomic group can yield more repeatable and accurate estimates of species' true, underlying DNA template proportions. These findings identify key factors that should be considered when designing studies that aim to apply metabarcoding data quantitatively.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14119"},"PeriodicalIF":5.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Designing Epigenetic Clocks for Wildlife Research. 为野生动物研究设计表观遗传时钟。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-05-06 DOI: 10.1111/1755-0998.14120
Levi Newediuk, Evan S Richardson, Alyssa M Bohart, Amélie Roberto-Charron, Colin J Garroway, Meaghan J Jones
{"title":"Designing Epigenetic Clocks for Wildlife Research.","authors":"Levi Newediuk, Evan S Richardson, Alyssa M Bohart, Amélie Roberto-Charron, Colin J Garroway, Meaghan J Jones","doi":"10.1111/1755-0998.14120","DOIUrl":"https://doi.org/10.1111/1755-0998.14120","url":null,"abstract":"<p><p>The applications of epigenetic clocks - statistical models that predict an individual's age based on DNA methylation patterns - are expanding in wildlife conservation and management. This growing interest highlights the need for field-specific design best practices. Here, we provide recommendations for two main applications of wildlife epigenetic clocks: estimating the unknown ages of individuals and assessing their biological ageing rates. Epigenetic clocks were originally developed to measure biological ageing rates of human tissues, which presents challenges for their adoption in wildlife research. Most notably, the estimated chronological ages of sampled wildlife can be unreliable, and sampling restrictions limit the number and variety of tissues with which epigenetic clocks can be constructed, reducing their accuracy. To address these challenges, we present a detailed workflow for designing, validating applying accurate wildlife epigenetic clocks. Using simulations and analyses applied to an extensive polar bear dataset from across the Canadian Arctic, we demonstrate that accurate epigenetic clocks for wildlife can be constructed and validated using a limited number of samples, accommodating projects with small budgets and sampling constraints. The concerns we address are critical for clock design, whether researchers or third-party service providers perform the bioinformatics. With our workflow and examples, we hope to support the accessible and widespread use of epigenetic clocks in wildlife conservation and management.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14120"},"PeriodicalIF":5.5,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unrecognised DNA Degradation in Flash-Frozen Genetic Samples in Natural History Collections. 自然历史藏品中速冻基因样本中未识别的DNA降解。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-05-05 DOI: 10.1111/1755-0998.14121
Alexander T Salis, Zachary Watson, Meghan Forcellati, Nasrin Ali, Shiva Karmakar, Jasleen Kaur, Nirhy Rabibisoa, Christopher J Raxworthy, Brian Tilston Smith
{"title":"Unrecognised DNA Degradation in Flash-Frozen Genetic Samples in Natural History Collections.","authors":"Alexander T Salis, Zachary Watson, Meghan Forcellati, Nasrin Ali, Shiva Karmakar, Jasleen Kaur, Nirhy Rabibisoa, Christopher J Raxworthy, Brian Tilston Smith","doi":"10.1111/1755-0998.14121","DOIUrl":"https://doi.org/10.1111/1755-0998.14121","url":null,"abstract":"<p><p>Optimal preservation of tissues from the field to long-term cryo-storage is paramount to securing genetic resources for research needs. DNA preservation techniques vary, with flash freezing currently considered the gold standard in tissue preservation. However, flash freezing tissue samples in the field presents challenges, necessitating a more comprehensive understanding of the quantity and quality of preserved DNA from different techniques in archival collections. We compared metrics from DNA extractions from field-collected amphibian, squamate and bird tissues from archival collections that were flash-frozen in liquid nitrogen or fixed in either ethanol or tissue lysis buffer prior to archival cryopreservation. We also included DNA extracted from tissues of known liquid nitrogen tank failures to provide a baseline of DNA degradation under the very worst-case scenario. Flash-frozen tissues often preserved higher yields of DNA, but peak fragment size, the percentage of fragments larger than 10 kb and DNA integrity numbers were all significantly reduced compared to tissues first preserved in fixative buffers. This pattern was observed across independent samples and between flash-frozen and buffer-preserved pair replicates. Degradation seen in flash-frozen tissues was also distinct to tissues from known tank failures. We suggest that degradation in flash-frozen tissues occurred during shipping, sample sorting/accession or during subsequent subsampling when tissues may partially or fully thaw, exposing DNA to damaging freeze-thaw processes. By contrast, tissues in fixative buffers were likely protected from freeze-thaw damage. This study highlights that using multiple field preservation methods and minimising freeze-thaw cycles for flash-frozen tissues may provide the most robust protection against the DNA degradation sources encountered by field collections.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14121"},"PeriodicalIF":5.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards Large-Scale Museomics Projects: A Cost-Effective and High-Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens. 迈向大规模博物馆组学项目:一种从博物馆昆虫标本中获得历史DNA的高成本效益和高通量提取方法。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-05-05 DOI: 10.1111/1755-0998.14117
Anna Holmquist, Holly Tavris, Grace Kim, Lauren Esposito, Brian Fisher, Athena Lam
{"title":"Towards Large-Scale Museomics Projects: A Cost-Effective and High-Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens.","authors":"Anna Holmquist, Holly Tavris, Grace Kim, Lauren Esposito, Brian Fisher, Athena Lam","doi":"10.1111/1755-0998.14117","DOIUrl":"https://doi.org/10.1111/1755-0998.14117","url":null,"abstract":"<p><p>Natural history collections serve as invaluable repositories of biodiversity data. Large-scale genomic analysis would greatly expand the utility and accessibility of museum collections, but the high cost and time-intensive nature of genomic methods limit such projects, particularly for invertebrate specimens. This paper presents an innovative, cost-effective and high-throughput approach for extracting genomic DNA from diverse insect specimens using single-phase reverse immobilisation (SPRI) beads. We optimised PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 4.0-11.6¢ per sample, cost dependent on sample type. Our method was validated against three widely used extraction protocols and showed comparable DNA yield and amplification success to the widely used Qiagen DNeasy kit. We successfully applied the protocol in a high-throughput manner, extracting DNA from 3786 insect specimens across a broad range of ages, taxonomies and tissue types. A detailed protocol and instructional video are provided to facilitate the adoption of the method by other researchers. By improving one of the most crucial steps in any molecular project, this SPRI bead-based DNA extraction approach has significant potential for enabling large-scale museomics projects, thereby increasing the utility of historical collections for biodiversity research and conservation efforts.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14117"},"PeriodicalIF":5.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations. 超越存在与缺失:利用eDNA和微卫星基因分型估计野生种群中微观生命形式的密度。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-05-02 DOI: 10.1111/1755-0998.14116
L M Liggan, K C Rolheiser, O Pontier, B Ramírez-Ibaceta, I Giménez, F Alberto
{"title":"Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations.","authors":"L M Liggan, K C Rolheiser, O Pontier, B Ramírez-Ibaceta, I Giménez, F Alberto","doi":"10.1111/1755-0998.14116","DOIUrl":"https://doi.org/10.1111/1755-0998.14116","url":null,"abstract":"<p><p>Many challenges arise when monitoring organisms with cryptic life-histories. For example, some cryptic life-stages are hard to identify or sample due to their microscopic nature, which creates unknowns surrounding an organism's population dynamics. Environmental DNA (eDNA) is a non-invasive sampling technique used to monitor cryptic species when traditional survey methods are challenging. Generally, eDNA has been used to quantify the presence/absence of species in various habitats. However, recent advances in high-throughput amplicon sequencing techniques have enabled researchers to detect intraspecific genetic diversity with eDNA. In this study, we present two complementary R packages that can be used to estimate the number of individuals in an eDNA sample. The first package (Amplicomsat) cleans high-throughput amplicon microsatellite sequences and counts the observed alleles identified in eDNA. Our second package (GenotypeQuant) then uses a numerical maximum likelihood estimator (NMLE) to estimate the number of contributors most likely to have produced the sequenced panel of microsatellite alleles amplified from eDNA. We first present simulations to characterise the accuracy and precision of the method. We then estimated densities of Nereocystis luetkeana (bull kelp) microscopic gametophytes from eDNA collected from an experiment with a manipulated number of gametophytes. Finally, we analysed benthic eDNA from kelp forest habitats. We found that gametophyte estimates produced by the NMLE varied within +3/-2 individuals when processing eDNA from rocks with 8 seeded gametophytes. We estimated 500 to 800 gametophytes·m<sup>-2</sup> densities in July, five or more months since spore germination and before the current year's spore release. Gametophyte abundance scaled with the sampling area and numbers were higher than total sporophyte densities.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14116"},"PeriodicalIF":5.5,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes. EukFunc:土壤真核生物自动分析的整体真核功能参考。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-04-30 DOI: 10.1111/1755-0998.14118
Guillaume Lentendu, David Singer, Sabine Agatha, Mohammad Bahram, S Emilia Hannula, Johannes Helder, Leho Tedersoo, Walter Traunspurger, Stefan Geisen, Enrique Lara
{"title":"EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.","authors":"Guillaume Lentendu, David Singer, Sabine Agatha, Mohammad Bahram, S Emilia Hannula, Johannes Helder, Leho Tedersoo, Walter Traunspurger, Stefan Geisen, Enrique Lara","doi":"10.1111/1755-0998.14118","DOIUrl":"https://doi.org/10.1111/1755-0998.14118","url":null,"abstract":"<p><p>The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14118"},"PeriodicalIF":5.5,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity. DNA元条形码与形态学方法在评估潮间带草皮和叶藻多样性中的应用。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-04-24 DOI: 10.1111/1755-0998.14115
Gabriela Borer, Cátia Monteiro, Fernando P Lima, Filipa M S Martins
{"title":"Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity.","authors":"Gabriela Borer, Cátia Monteiro, Fernando P Lima, Filipa M S Martins","doi":"10.1111/1755-0998.14115","DOIUrl":"https://doi.org/10.1111/1755-0998.14115","url":null,"abstract":"<p><p>Large biogeographical shifts in marine communities are taking place in response to climate change and biological invasions yet we still lack a full understanding of their diversity and distribution. An important example of this is turf and foliose algae that are key coastal primary producers in several regions and are expanding into new environments. Traditionally, monitoring turf and foliose algae communities involves species identification based on morphological traits, which is challenging due to their reduced dimensions and highly variable morphology. Molecular methods promise to revolutionise this field, but their effectiveness in detecting turf and foliose algae has yet to be tested. Here, we evaluate the performance of DNA metabarcoding (COI and rbcL markers) and morphological identification (in situ and photoquadrat) to describe intertidal turf and foliose algae communities along the Portuguese coast. Both molecular markers detected more taxa than the morphological methods and showed greater discrimination of turf and foliose algae communities between regions, matching our knowledge of the geographical and climatic patterns for the region. In sum, our multi-marker metabarcoding approach was more efficient than morphology-based methods in characterising turf and foliose algae communities along the Portuguese coast, differentiating morphologically similar species, and detecting unicellular organisms. However, certain taxa that were identified by in situ and photoquadrat approaches were not detected through metabarcoding, partly due to lack of reference barcodes or taxonomic resolution. Metabarcoding emerges as a valuable tool for monitoring these communities, particularly in long-term programmes requiring accuracy, speed, and reproducibility.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14115"},"PeriodicalIF":5.5,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies. 海洋脊椎动物eDNA研究中分类器的综合评价。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-04-17 DOI: 10.1111/1755-0998.14107
Philipp E Bayer, Adam Bennett, Georgia Nester, Shannon Corrigan, Eric J Raes, Madalyn Cooper, Marcelle E Ayad, Philip McVey, Anya Kardailsky, Jessica Pearce, Matthew W Fraser, Priscila Goncalves, Stephen Burnell, Sebastian Rauschert
{"title":"A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.","authors":"Philipp E Bayer, Adam Bennett, Georgia Nester, Shannon Corrigan, Eric J Raes, Madalyn Cooper, Marcelle E Ayad, Philip McVey, Anya Kardailsky, Jessica Pearce, Matthew W Fraser, Priscila Goncalves, Stephen Burnell, Sebastian Rauschert","doi":"10.1111/1755-0998.14107","DOIUrl":"https://doi.org/10.1111/1755-0998.14107","url":null,"abstract":"<p><p>Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14107"},"PeriodicalIF":5.5,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143953435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis. bestRAD测序方法的优化与评价——用于确定东方小实蝇(Bactrocera dorsalis)入侵途径
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-04-11 DOI: 10.1111/1755-0998.14114
Emeline Charbonnel, Laure Benoit, Sabine Nidelet, Enrique Ortega-Abboud, Bernhard Gschloessl, Raphaël Leblois, David Ouvrard, Marie-Pierre Chapuis
{"title":"Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis.","authors":"Emeline Charbonnel, Laure Benoit, Sabine Nidelet, Enrique Ortega-Abboud, Bernhard Gschloessl, Raphaël Leblois, David Ouvrard, Marie-Pierre Chapuis","doi":"10.1111/1755-0998.14114","DOIUrl":"https://doi.org/10.1111/1755-0998.14114","url":null,"abstract":"<p><p>The bestRAD technique is a reduced genome representation approach with high-capacity sample multiplexing and physical isolation of biotin-labelled target DNA fragments using streptavidin beads, which should reduce total cost and genotyping errors. While we here formalise the relevance of this approach within the HTS landscape, our foremost aim was to improve its replicability, validity, and transparency. We first optimised the molecular laboratory protocol and shared the associated protocols (e.g., final detailed methodologies, quality control, best practices) under the FAIR principles. Using 84 worldwide individual samples of the Oriental fruit fly, Bactrocera dorsalis, a major invasive pest, we revealed a low rate of PCR duplicates, robustness to DNA quality and quantity, high genotype call rate, insignificant genotyping error rate, high nuclear and mitochondrial genome representativeness, and a high level of genetic information. This in-depth data quality assessment, along with total cost and handling time reduced by an estimated one-third relative to the parent RAD-Seq version, demonstrates that bestRAD is an excellent compromise between cost and quality. While we generated high-quality genomic resources for B. dorsalis, we also share details and recommendations for the bestRAD technique that can be readily used in any laboratory and applied to all organisms, even without published genome sequence.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14114"},"PeriodicalIF":5.5,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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