Molecular Ecology Resources最新文献

{"title":"Correcting for Bias in Estimates of \u0000 \u0000 \u0000 \u0000 θ\u0000 w\u0000 \u0000 \u0000 and Tajima's \u0000 \u0000 \u0000 D\u0000 \u0000 From Missing Data in Next-Generation Sequencing","authors":"Nick Bailey,&nbsp;Laurie Stevison,&nbsp;Kieran Samuk","doi":"10.1111/1755-0998.14104","DOIUrl":"10.1111/1755-0998.14104","url":null,"abstract":"<p>Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>θ</mi>\u0000 <mi>w</mi>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math>) of genetic diversity, and Tajima's <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>D</mi>\u0000 </mrow>\u0000 </semantics></math>, used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (<span>VCFtools</span>, <span>PopGenome</span>, <span>pegas</span> and <span>scikit-allel</span>). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>θ</mi>\u0000 <mi>w</mi>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> across programs. We found a consequent bias in estimates of Tajima's <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>D</mi>\u0000 </mrow>\u0000 </semantics></math>, though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular <span>pixy</span> software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High-Throughput Nanofluidic Chip Technology: Species-Specific qPCR Assay Panel Development and Validation.","authors":"Matthew R Charron, Matthew C Yates, Daniel D Heath","doi":"10.1111/1755-0998.14106","DOIUrl":"https://doi.org/10.1111/1755-0998.14106","url":null,"abstract":"<p><p>Stomach content DNA (scDNA) analyses have become the standard practice for measuring trophic interactions. scDNA metabarcoding has provided broadscale diet composition data but can potentially underestimate certain prey species, as many of the recovered sequence reads come from predator-derived DNA, potentially resulting in incomplete diet information. Targeted detection (quantitative real-time PCR-qPCR) strategies allow for single-species detection from complex multispecies scDNA mixtures. A recent advancement in qPCR technology, high-throughput qPCR (HT-qPCR), allows simultaneous multispecies targeted detection and quantification of candidate species. Here, we describe the development and validation of a panel of single-species qPCR assays targeting the CO1 region of 28 prey fishes from the Great Lakes. We performed a three-step validation procedure for all assays using high-throughput OpenArray nanofluidic technology, measuring assay sensitivity, specificity and interference. Specifically, all assays were measured against dilution series of both target and non-target species DNA with detection limits ranging from 0.00503 pg to 0.0221 ng template DNA per reaction. Assays were tested for interference (e.g., PCR inhibitor) effects by creating artificial scDNA samples spiked with serially diluted target species DNA, resulting in a range of reduction in sensitivity (range = 0.0-125x fold). We validated the OpenArray qPCR assays using individual full-reaction TaqMan qPCR for nine of the assays, finding similar sensitivity despite expectations for the loss of sensitivity in the nanoscale reactions. HT-qPCR targeted detection has the potential to revolutionise scDNA (and eDNA) monitoring by significantly reducing laboratory effort to provide sensitive, targeted and quantitative detection data for multiple species simultaneously.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14106"},"PeriodicalIF":5.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672930","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}

{"title":"Cochlear Cell Atlas of Two Laryngeal Echolocating Bats—New Evidence for the Adaptive Nervous Physiology in Constant Frequency Bat","authors":"Xue Wang,&nbsp;Mingyue Bao,&nbsp;Hui Wang,&nbsp;Ruyi Sun,&nbsp;Wentao Dai,&nbsp;Keping Sun,&nbsp;Yue Zhu,&nbsp;Yingting Pu,&nbsp;Yujia Chu,&nbsp;Xintong Li,&nbsp;Tianhui Wang,&nbsp;Minjie Zhang,&nbsp;Aiqing Lin,&nbsp;Jiqian Li,&nbsp;Jiang Feng","doi":"10.1111/1755-0998.14101","DOIUrl":"10.1111/1755-0998.14101","url":null,"abstract":"<p>Bats have evolved highly adapted auditory mechanisms associated with ecological specialisation. However, there is scattered knowledge about the neurophysiological and cellular basis underlying high-frequency hearing in echolocating bats. Herein, the total cochlear cell atlas of <i>Rhinolophus ferrumequinum</i> (constant frequency (CF) bat) and <i>Myotis pilosus</i> (frequency modulated (FM) bat) was conducted using the 10x Genomics single-nucleus RNA sequencing method. Differences in the proportion of cochlear cell types, especially for the neural cells, were detected between these two bat species. Previously, genes upregulated in the cochlea of CF compared with FM bats, were found to be mostly related to nervous activities. After mapping to the cochlear cell atlas, we found that the upregulated genes were from neural cells, lateral wall cells and neurosensory epithelium cells. A class of specific neurons and associated functions was detected in the cochlea of <i>R. ferrumequinum</i>, revealed by cross-species single-cell transcriptomic analyses. Furthermore, molecular evidence for the differentiation from glial cells to neuronal cells was also uncovered in the cochlea of <i>R. ferrumequinum</i>. Overall, this study identified specific cellular molecular properties that constitute the neuroanatomical evolutionary dynamics underlying distinct echolocating types of bats and provided new molecular evidence for high-frequency hearing of echolocating bats, promoting related studies about ecological adaptation and evolution.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems","authors":"Silke Van den Wyngaert,&nbsp;Slawek Cerbin,&nbsp;Laura Garzoli,&nbsp;Hans-Peter Grossart,&nbsp;Alena S. Gsell,&nbsp;Alexandra Kraberg,&nbsp;Cécile Lepère,&nbsp;Sigrid Neuhauser,&nbsp;Miloš Stupar,&nbsp;Andrea Tarallo,&nbsp;Michael Cunliffe,&nbsp;Claire Gachon,&nbsp;Ana Gavrilović,&nbsp;Hossein Masigol,&nbsp;Serena Rasconi,&nbsp;Géza B. Selmeczy,&nbsp;Dirk S. Schmeller,&nbsp;Bettina Scholz,&nbsp;Natàlia Timoneda,&nbsp;Ivana Trbojević,&nbsp;Elżbieta Wilk-Woźniak,&nbsp;Albert Reñé","doi":"10.1111/1755-0998.14099","DOIUrl":"10.1111/1755-0998.14099","url":null,"abstract":"<p>Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius","authors":"Sailan Liu,&nbsp;Yan Gao,&nbsp;Xinrui Long,&nbsp;Kunhuan Li,&nbsp;Qilin Gutang,&nbsp;Huiying Xie,&nbsp;Jingzhen Wang,&nbsp;Jiashen Tian,&nbsp;Bo Liang,&nbsp;Jianqing Lin,&nbsp;Wenhua Liu","doi":"10.1111/1755-0998.14103","DOIUrl":"10.1111/1755-0998.14103","url":null,"abstract":"<div>\u0000 \u0000 <p>Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not easy for marine fish, especially those with long-distance migration abilities. In this study, we constructed a high-quality reference genome for Japanese Spanish mackerel (<i>Scomberomorus niphonius</i>) and explored its population structure using whole genomic and epigenomic data. Despite the high depth of the sequence data, we failed to identify geographical genetic differentiation of Japanese Spanish mackerel across Chinese coastal waters. However, whole-genome bisulphite sequencing can classify this species into the Bohai–Yellow Sea group and the East China Sea–South China Sea group. Genes involved in embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations and may play important roles as drivers of population structure in Japanese Spanish mackerel. Our study not only provides the first reference genome of the Japanese Spanish mackerel and sheds light on population differentiation at the epigenomic level, but also provides a methylome-based framework for population structure analyses of marine fish with long-distance migration ability. These findings are expected to facilitate the development of scientific programmes for the successful conservation of marine fishery resources.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623052","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}

{"title":"Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data","authors":"Stephanie D. Jurburg","doi":"10.1111/1755-0998.14102","DOIUrl":"10.1111/1755-0998.14102","url":null,"abstract":"<p>16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (&lt; 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14102","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat","authors":"Luis P. da Silva,&nbsp;Miguel Porto,&nbsp;Francisco Amorim,&nbsp;Pedro Beja,&nbsp;Vanessa A. Mata","doi":"10.1111/1755-0998.14100","DOIUrl":"10.1111/1755-0998.14100","url":null,"abstract":"<div>\u0000 \u0000 <p>DNA metabarcoding is increasingly used in dietary studies, but it has limitations, such as detecting nonfood taxa. This issue is frequently mentioned in the literature but poorly understood, limiting interpretation of results and mitigation strategies. We evaluate the extent and sources of nonfood plant DNA in dietary metabarcoding, based on 281 faecal samples of a strictly insectivorous bat. We modelled plant taxa detections in relation to pollination syndromes, flowering and fruiting phenology and habitat associations, and we estimated co-occurrences between plants and arthropods. The bat arthropod diet was consistent with previous studies. Plants were detected in 82.9% of samples, representing 148 taxa, and all pollination syndromes evaluated. Plant detections were more frequent during their flowering periods, particularly for those with mixed pollination syndromes, suggesting a relationship between flowering and detectability. Fruiting had a positive, albeit weaker, effect. There was a tendency for more frequent detection of forest plants and less frequent detection of plants associated with riparian and agricultural habitats. Co-occurrences between arthropods and plants were weak and inconsistent. Our results highlight the potential for widespread detection of nonfood plant DNA in metabarcoding studies, calling for great care when analysing the plant component of diets. Specifically, we recommend: (i) implementing strategies for reducing plant contamination during field sampling; (ii) using multiple field and lab negative controls; and (iii) using ancillary information (e.g., sample visual inspection and literature review) to aid interpretation of metabarcoding results. Moreover, we recommend that studies reporting plant consumption results greatly diverging from dietary patterns obtained through other methods should include detailed explanations of methodological steps taken to exclude the confounding effects of nonfood plant DNA.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603277","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}

{"title":"EntoSieve: Automated Size-Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding","authors":"Aleida Ascenzi,&nbsp;Lorenz Wührl,&nbsp;Vivian Feng,&nbsp;Nathalie Klug,&nbsp;Christian Pylatiuk,&nbsp;Pierfilippo Cerretti,&nbsp;Rudolf Meier","doi":"10.1111/1755-0998.14097","DOIUrl":"10.1111/1755-0998.14097","url":null,"abstract":"<p>Widespread insect decline necessitates the development and use of standardized protocols for regular monitoring. These methods have to be rapid, efficient and cost-effective to allow for large-scale implementation. Many insect sampling and molecular methods have been developed. These include Malaise trapping, high-throughput DNA barcoding (‘megabarcoding’) and metabarcoding. The latter allows for assessing the species diversity in whole samples using few steps, but sample heterogeneity in terms of body size remains a challenge since large insects contribute disproportionately more mtDNA than small ones. This can potentially overwhelm the template DNA from small species that then go undetected. Size-sorting can mitigate this problem, but no satisfying automated, rapid and non-destructive solutions are available. We introduce the EntoSieve, a low-cost and DIY motorized instrument that disentangles and sorts abundant insect bulk samples into several body size fractions while minimizing damage to specimens, thus reducing the risk of DNA contamination across size fractions (e.g. legs of large specimens in small body size fraction). EntoSieve utilizes readily available components, 3D-printed parts and customizable meshes, thus enabling parallelization at low cost. We here show the efficiency of the EntoSieve for three samples with more than 10,000 specimens using three sieving protocols and assess the impact on specimen integrity. Efficiency ranged from 92% to 99%, achieved within 18–60 min, and specimen damage was not significant for subsamples. By facilitating rapid pre-processing, the device contributes to producing morphologically valuable vouchers for megabarcoding and is likely to improve compositional diversity accuracy across size classes when using metabarcoding.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14097","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment","authors":"K. Birchard,&nbsp;C. Boccia,&nbsp;H. Lounder,&nbsp;L. Colston-Nepali,&nbsp;V. L. Friesen","doi":"10.1111/1755-0998.14096","DOIUrl":"10.1111/1755-0998.14096","url":null,"abstract":"<p>The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present <i>popfinder:</i> a new, easy-to-use <i>Python</i>-based artificial neural network pipeline for genetic population assignment. We tested <i>popfinder</i> both with simulated genetic data from populations connected by varying levels of gene flow and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. <i>Popfinder</i> was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, <i>popfinder</i> was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, <i>popfinder</i> provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14096","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies","authors":"Yiqiu Lu,&nbsp;Yuran Dong,&nbsp;Min Zhang,&nbsp;Lingfeng Mao","doi":"10.1111/1755-0998.14095","DOIUrl":"10.1111/1755-0998.14095","url":null,"abstract":"<div>\u0000 \u0000 <p>Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571621","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}