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A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.). 利用eDNA和eRNA的元组学方法评估西部蜜蜂蜂王浆相关生物群落。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-27 DOI: 10.1111/1755-0998.14090
Jennifer M Standley, Jose Marcelino, Fahong Yu, James D Ellis
{"title":"A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).","authors":"Jennifer M Standley, Jose Marcelino, Fahong Yu, James D Ellis","doi":"10.1111/1755-0998.14090","DOIUrl":"https://doi.org/10.1111/1755-0998.14090","url":null,"abstract":"<p><p>Royal jelly (RJ) is a glandular secretion fed to developing honey bee larvae by adult worker bees. It is also a potential source of disease transmission in and between honey bee colonies. We endeavored to characterize the microbiome, virome, and other biota present in RJ via an integrated meta-omics approach. Using a magnetic beads-based extraction protocol, we identified eDNA and eRNA fragments from organisms of interest in RJ using high-throughput metagenomics (DNA-seq), metatranscriptomics (total RNA-seq), and parallel sequencing. This allowed us to enhance the detection of Operational Taxonomic Units (OTUs) undetectable by standard 'omics or amplicon protocols'. Using this integrated approach, we detected OTUs present in RJ from honey bee pests and pathogens, including Melissococcus plutonius, Paenibacillus larvae, Varroa destructor, V. jacobsoni, Aethina tumida, Galleria mellonella, Vairimorpha ceranae, Apis mellifera filamentous virus, Black queen cell virus, Acute bee paralysis virus, Sacbrood virus, Deformed wing virus, Israeli acute bee paralysis virus, Kashmir bee virus, and Slow bee paralysis virus, as well as multiple beneficial gut bacteria from the genera Lactobacillus, Actinobacteria, and Gluconobacter. The presence of DNA and RNA from these organisms does not conclusively indicate the presence of live organisms in the RJ, but it does suggest some exposure of the RJ to these organisms. The results present a comprehensive eDNA and eRNA microbial profile of RJ, demonstrating that our novel method is an effective and sensitive molecular tool for high-resolution metagenomic and metatranscriptomic profiling, and is of value for detection of pathogens of concern for the beekeeping industry.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14090"},"PeriodicalIF":5.5,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514280","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
Dung Beetle iDNA Provides an Effective Way to Detect Diverse Mycological Communities. 蜣螂 iDNA 为检测多样化的真菌群落提供了一种有效方法。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-26 DOI: 10.1111/1755-0998.14091
Thilina S Nimalrathna, Huan Fan, Ahimsa Campos-Arceiz, Akihiro Nakamura
{"title":"Dung Beetle iDNA Provides an Effective Way to Detect Diverse Mycological Communities.","authors":"Thilina S Nimalrathna, Huan Fan, Ahimsa Campos-Arceiz, Akihiro Nakamura","doi":"10.1111/1755-0998.14091","DOIUrl":"https://doi.org/10.1111/1755-0998.14091","url":null,"abstract":"<p><p>Fungi play crucial ecological and economic roles, yet their diversity and distribution remain poorly known and challenging to assess. Using recent advances in invertebrate-derived DNA (iDNA) for biodiversity monitoring, we investigated the potential of dung beetle iDNA for fungal sampling and monitoring. We sampled two habitats (rainforest vs. rubber plantation) and seasons (dry vs. rainy) in tropical Xishuangbanna, southwest China. We extracted, amplified and identified 9259 unique fungi Amplicon Sequence Variants (ASVs) from the gut of three species of dung beetles (Paragymnopleurus sp., telecoprids; Onthophagus diabolicus, paracoprids; and Onthophagus cf. gracilipes, endocoprids). Fungal community composition was different across habitats and seasons, with the highest diversity found in the rainy season rainforest. Our results were consistent with previous eDNA-based studies based on soil samples in the detection of habitat differences (both approaches were able to detect low diversity of Basidiomycota in rubber plantations). However, our approach outperformed soil-based eDNA studies in being able to detect fungal occurrences associated with seasonal precipitation patterns. Our findings highlight the utility of dung beetle iDNA to uncover spatiotemporal dynamics of fungal communities across different habitats. The use of iDNA broadens fungal biodiversity research, strengthens fungal monitoring to assess anthropogenic impacts and presents opportunities to conserve fungal diversity.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14091"},"PeriodicalIF":5.5,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497735","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
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra. 从站点频谱推断单一人口统计历史的贝叶斯阶梯图。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-26 DOI: 10.1111/1755-0998.14087
Sebastian Höhna, Ana Catalán
{"title":"Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra.","authors":"Sebastian Höhna, Ana Catalán","doi":"10.1111/1755-0998.14087","DOIUrl":"https://doi.org/10.1111/1755-0998.14087","url":null,"abstract":"<p><p>The StairwayPlot approach provides an elegant, flexible and powerful method to estimate complex demographic histories of single populations from site frequency spectrum data. It uses expected coalescent times to compute the expected site frequency spectrum within a multinomial likelihood function. Population sizes are allowed to vary freely between coalescent events but are constant within each interval. Here, we implement the StairwayPlot approach in the Bayesian software package RevBayes. We use approaches developed for Bayesian Skyline Plots, which include independent and identically distributed (i.i.d.) population sizes, Gaussian Markov random fields and Horseshoe Markov random fields as prior distributions on population sizes. Furthermore, we implement a recently developed approach for computing the leave-one-out cross-validation probability for efficient model selection. We compare inference from our Bayesian implementation to the original Maximum Likelihood implementation, StairwayPlot2. Our results show that our Bayesian implementation in RevBayes performs comparable to StairwayPlot2 in terms of parameter accuracy, which is expected given that both use the same underlying likelihood function. From our set of prior models, the Gaussian Markov random field prior performed best for smoothly varying demographic histories, while the Horseshoe Markov random field performs best for abruptly changing demographic histories. We conclude the study by exploring several choices often faced in empirical studies, including the estimate of the total sequence length, the assumed mutation rate, as well as biases through mis-calling ancestral alleles. We show using our empirical example that as few as 10 diploid individuals are sufficient to infer complex demographic histories, but at least 500 k single nucleotide polymorphisms (SNPs) are required.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14087"},"PeriodicalIF":5.5,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514282","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
Selecting Competent Reverse Transcription Strategies to Maximise Biodiversity Recovery With eRNA Metabarcoding. 选择合适的逆转录策略,最大限度地利用eRNA元条形码恢复生物多样性。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-22 DOI: 10.1111/1755-0998.14092
Fuwen Wang, Wei Xiong, Xuena Huang, Aibin Zhan
{"title":"Selecting Competent Reverse Transcription Strategies to Maximise Biodiversity Recovery With eRNA Metabarcoding.","authors":"Fuwen Wang, Wei Xiong, Xuena Huang, Aibin Zhan","doi":"10.1111/1755-0998.14092","DOIUrl":"https://doi.org/10.1111/1755-0998.14092","url":null,"abstract":"<p><p>Both environmental DNA (eDNA) and environmental RNA (eRNA) have been widely adopted for biodiversity assessment. While eDNA often persists longer in environments, eRNA offers a more current view of biological activities. In eRNA metabarcoding, extracted eRNA is reverse transcribed into complementary DNA (cDNA) for metabarcoding. However, the efficacy of various reverse transcription strategies has not been evaluated. Here we compared the biodiversity recovery efficiency of three strategies: random priming with hexamers, oligo(dT) priming and taxa-specific priming using Mifish-U for fish in both high- and low-biodiversity regions. Our results demonstrate that reverse transcription strategies significantly impact biodiversity recovery. Random priming consistently detected the highest number of taxa in both low- and high-biodiversity regions. In low-biodiversity areas, oligo(dT) performed comparably to random hexamers; however, in high-biodiversity regions, random hexamers outperformed oligo(dT), particularly in recovering rare taxa. While taxa-specific priming was comparable to the other strategies for high-abundance taxa, it was less effective for rare taxa, thus limiting its utility for comprehensive biodiversity assessment. These differences are largely due to the multiple binding sites for random hexamers compared to the fewer or absent sites with oligo(dT) and taxa-specific primers under high eRNA degradation. Combining random hexamers and oligo(dT) significantly improved taxa recovery, especially for low-abundance species, supporting its best practice in eukaryotes. For prokaryotes or genes lacking polyadenylation, random priming is favoured over taxa- or gene-specific priming. Collectively, these findings underscore the critical importance of selecting appropriate reverse transcription strategies in eRNA metabarcoding, with significant implications for effective biodiversity monitoring and conservation efforts.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14092"},"PeriodicalIF":5.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476185","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
Correction to “Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae)” 更正“三个新的蜘蛛基因组揭示了蜘蛛的多样化和Hox集群结构:Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae)和Cheiracanthium punctorium (Cheiracanthiidae)”
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-22 DOI: 10.1111/1755-0998.14093
{"title":"Correction to “Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae)”","authors":"","doi":"10.1111/1755-0998.14093","DOIUrl":"10.1111/1755-0998.14093","url":null,"abstract":"<p>Schöneberg, Y., T. L. Audisio, A. Ben Hamadou, M. Forman, J. Král, T. Kořínková, E. Líznarová, C. Mayer, L. Prokopcová, H. Krehenwinkel, S. Prost, and S. Kennedy. 2025. “Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: <i>Ryuthela nishihirai</i> (Liphistiidae), <i>Uloborus plumipes</i> (Uloboridae) and <i>Cheiracanthium punctorium</i> (Cheiracanthiidae).” <i>Molecular Ecology Resources</i> 25: e14038.</p><p>In the list of authors, J. Král's link to the address of his institution is incorrect. Instead of ‘Jiří Král<sup>6</sup>’, it should read ‘Jiří Král<sup>5</sup>’. J. Král is a member of Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic.</p><p>We apologise for this error.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14093","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476184","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}
引用次数: 0
A Molecular Survey of the Occurrence of Coffee Berry Disease Resistant Coffee Cultivars Near the Wild Gene Pool of Arabica Coffee in Its Region of Origin in Southwest Ethiopia. 埃塞俄比亚西南部阿拉比卡咖啡产地野生基因库附近咖啡浆果抗病品种发生的分子调查
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-21 DOI: 10.1111/1755-0998.14085
Yves Bawin, Beyene Zewdie, Biruk Ayalew, Isabel Roldán-Ruiz, Steven B Janssens, Ayco J M Tack, Sileshi Nemomissa, Kassahun Tesfaye, Kristoffer Hylander, Olivier Honnay, Tom Ruttink
{"title":"A Molecular Survey of the Occurrence of Coffee Berry Disease Resistant Coffee Cultivars Near the Wild Gene Pool of Arabica Coffee in Its Region of Origin in Southwest Ethiopia.","authors":"Yves Bawin, Beyene Zewdie, Biruk Ayalew, Isabel Roldán-Ruiz, Steven B Janssens, Ayco J M Tack, Sileshi Nemomissa, Kassahun Tesfaye, Kristoffer Hylander, Olivier Honnay, Tom Ruttink","doi":"10.1111/1755-0998.14085","DOIUrl":"https://doi.org/10.1111/1755-0998.14085","url":null,"abstract":"<p><p>Cultivation of crops close to their wild relatives may jeopardise the integrity of wild genetic resources. Detecting cultivars among wild plants is necessary to characterise crop-wild gene flow, but can be challenging if cultivars and wild plants are phenotypically highly similar. Genomics tools can be used instead, but the selection of diagnostic loci for cultivar identification can be difficult if the wild and cultivated genepools are closely related. In Ethiopia, Arabica coffee cultivars resistant to coffee berry disease (CBD) occur near wild Coffea arabica plants and local landraces. However, the abundance and distribution of these cultivars across coffee sites remains unclear. Here, we present a new module of the SMAP package called SMAP relatedness pairwise to characterise pairwise genetic relationships between individuals based on haplotype calls and to identify diagnostic loci that distinguish (sets of) individuals from each other. Next, we estimate the relative abundance of CBD-resistant cultivars across 60 Ethiopian Arabica coffee sites using a genome-wide fingerprinting approach. We confirm the presence of these cultivars in around 75% of the coffee sites with a high agreement between a field survey and our DNA fingerprinting approach. At least 20 out of 60 sites with supposedly wild C. arabica individuals contain signatures of the cultivated genepool. Overall, we conclude that CBD-resistant cultivars are widespread in Ethiopian coffee sites. The development of SMAP relatedness pairwise opens opportunities to assess the distribution of coffee cultivars in other regions in Ethiopia and to apply similar screenings near wild relatives from other crops.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14085"},"PeriodicalIF":5.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466406","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
Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA. 导航过去的海洋:比较海洋古代沉积物环境DNA的元条形码和宏基因组学。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-20 DOI: 10.1111/1755-0998.14086
Luke E Holman, Giulia Zampirolo, Richard Gyllencreutz, James Scourse, Tobias Frøslev, Christian Carøe, Shyam Gopalakrishnan, Mikkel Winther Pedersen, Kristine Bohmann
{"title":"Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.","authors":"Luke E Holman, Giulia Zampirolo, Richard Gyllencreutz, James Scourse, Tobias Frøslev, Christian Carøe, Shyam Gopalakrishnan, Mikkel Winther Pedersen, Kristine Bohmann","doi":"10.1111/1755-0998.14086","DOIUrl":"https://doi.org/10.1111/1755-0998.14086","url":null,"abstract":"<p><p>The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14086"},"PeriodicalIF":5.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466409","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 Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors. 双翅目疾病媒介生态监测的短读扩增子测序方案和生物信息学管道。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-18 DOI: 10.1111/1755-0998.14088
Raquel Lima-Cordón, Jason Travis Mohabir, Mohini Sooklall, Aina Martinez Zurita, Meg Shieh, Cheyenne Knox, Sabrina Gobran, Zachary Johnson, Margaret Laws, Ruchit Panchal, Reza Niles-Robin, Horace Cox, Maria Eugenia Grillet, Jorge E Moreno, Socrates Herrera, Martha Quinones, Angela M Early, Jacob A Tennessen, Daniel E Neafsey
{"title":"A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.","authors":"Raquel Lima-Cordón, Jason Travis Mohabir, Mohini Sooklall, Aina Martinez Zurita, Meg Shieh, Cheyenne Knox, Sabrina Gobran, Zachary Johnson, Margaret Laws, Ruchit Panchal, Reza Niles-Robin, Horace Cox, Maria Eugenia Grillet, Jorge E Moreno, Socrates Herrera, Martha Quinones, Angela M Early, Jacob A Tennessen, Daniel E Neafsey","doi":"10.1111/1755-0998.14088","DOIUrl":"10.1111/1755-0998.14088","url":null,"abstract":"<p><p>Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14088"},"PeriodicalIF":5.5,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439439","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
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data detecve:快速、灵敏、精确地检测基因组数据中的内源性病毒元素。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-12 DOI: 10.1111/1755-0998.14083
Nadja Brait, Thomas Hackl, Sebastian Lequime
{"title":"detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data","authors":"Nadja Brait,&nbsp;Thomas Hackl,&nbsp;Sebastian Lequime","doi":"10.1111/1755-0998.14083","DOIUrl":"10.1111/1755-0998.14083","url":null,"abstract":"<p>Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce <i>detectEVE</i>, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. <i>detectEVE</i> deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that <i>detectEVE</i> is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 4","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14083","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397585","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}
引用次数: 0
Correction to “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach” “量化线粒体异质性多样性:计算方法”的勘误表。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-02-12 DOI: 10.1111/1755-0998.14089
{"title":"Correction to “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach”","authors":"","doi":"10.1111/1755-0998.14089","DOIUrl":"10.1111/1755-0998.14089","url":null,"abstract":"<p>Liu, K., N. Xie, and Y. Wang. 2024. “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach.” <i>Molecular Ecology Resources</i> 24, no. 1: e13874. https://doi.org/10.1111/1755-0998.13874.</p><p>The authors reported the Pearson correlation coefficient but incorrectly used the symbol <i>R</i><sup>2</sup> instead of <i>R</i> for the correlation coefficient. Consequently, the relevant text and figures (Figures 3 and 4) need to be revised accordingly. Additionally, the phrase ‘exceeding the reported <i>R</i><sup>2</sup> value for allele frequency correlations’ should be deleted from the abstract. In the discussion section, the phrase ‘higher than the reported <i>R</i><sup>2</sup> value of 0.29 for allele frequency between mothers and children in Rebolledo-Jaramillo et al. (2014)’ should also be deleted.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14089","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397661","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}
引用次数: 0
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