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Unveiling the Hidden Feast: A Model to Translate Molecular Detection Into Predation Rate-Application Example on Biological Control by Generalist Predators in Agricultural Fields. 揭开隐藏的盛宴:一种将分子检测转化为捕食率的模型——在农业领域多面手生物防治中的应用实例。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-20 DOI: 10.1111/1755-0998.70033
Abel Masson, Kévan Rastello, Ambre Sacco-Martret de Préville, Yann Tricault, Sylvain Poggi, Elsa Canard, Marie-Pierre Etienne, Manuel Plantegenest
{"title":"Unveiling the Hidden Feast: A Model to Translate Molecular Detection Into Predation Rate-Application Example on Biological Control by Generalist Predators in Agricultural Fields.","authors":"Abel Masson, Kévan Rastello, Ambre Sacco-Martret de Préville, Yann Tricault, Sylvain Poggi, Elsa Canard, Marie-Pierre Etienne, Manuel Plantegenest","doi":"10.1111/1755-0998.70033","DOIUrl":"https://doi.org/10.1111/1755-0998.70033","url":null,"abstract":"<p><p>Few processes are as decisive as predation in shaping the structure and dynamics of ecological communities. For most predator species, however, the number of prey items killed by a predator in a day (predation rate) remains impossible to assess because direct observations are scarce or impossible to acquire. For such species, molecular gut content analyses are routinely used to test for the presence of a prey in the predator's gut. Specifically, our model uses a novel mechanistic representation of predation and digestion to integrate field data on prey detection and laboratory data on prey molecular signal decay in the predator's gut. Model fit provides an estimate of the slope and intercept of the digestion curve (molecular signal decay) and an estimate of the predation rate. In a case study targeting 25 carabid beetle species and 5 types of prey in agricultural fields (winter wheat), we use our model to estimate predation rates for each predator-prey pair. Based on predation rate estimates, we introduce a new biocontrol indicator at community scale and explore its potential for advanced agroecological research. We discuss the performance of our model on the basis of the scant information available in the literature and detail its conditions of application to highlight its advantages over existing predation models.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70033"},"PeriodicalIF":5.5,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937500","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
Revisiting Genetic Data Stewardship Practices in Aotearoa New Zealand: A Call to Action on Integrating Māori Data Sovereignty. 重新审视新西兰奥特罗阿的遗传数据管理实践:关于整合Māori数据主权的行动呼吁。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-19 DOI: 10.1111/1755-0998.70021
Manpreet K Dhami, Paige Matheson, Starsha Bird, Leilani Walker, Holden Hohaia, Angela McGaughran
{"title":"Revisiting Genetic Data Stewardship Practices in Aotearoa New Zealand: A Call to Action on Integrating Māori Data Sovereignty.","authors":"Manpreet K Dhami, Paige Matheson, Starsha Bird, Leilani Walker, Holden Hohaia, Angela McGaughran","doi":"10.1111/1755-0998.70021","DOIUrl":"10.1111/1755-0998.70021","url":null,"abstract":"<p><p>Genetic data, including environmental DNA (eDNA), are regularly used to monitor escalating biodiversity concerns globally. In Aotearoa New Zealand, biodiversity is unique and cherished-many species are taonga (treasured) and cared for by kaitiaki (guardians with customary responsibilities), specifically mana whenua with custodial rights (Māori; the Indigenous people of New Zealand). Discussions are currently underway regarding the development of a reference DNA barcode database for biodiversity in Aotearoa New Zealand to improve outcomes for biosecurity surveillance and biodiversity assessment. A priority of these discussions is that the database development and eventual implementation accords with Te Tiriti o Waitangi (The Treaty of Waitangi). Here, we evaluate current practices for storing genetic data from samples collected in Aotearoa New Zealand by examining two major public data repositories-the National Centre for Biotechnology Information (NCBI) GenBank and the Barcode of Life Data System (BOLD). We find that current database practices limit opportunities for Māori data sovereignty, with DNA from many taonga species uploaded to public repositories with no associated restrictions or guidelines over use. This is an important finding that will help shape the development of a future DNA reference database for Aotearoa New Zealand that integrates the rights and interests of Indigenous communities.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70021"},"PeriodicalIF":5.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870590","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
Heterogametic Females Reveal a ZW Sex Determination System and a Putative Sex Chromosome for the Chilean Jack Mackerel, Trachurus murphyi. 智利长尾鲭鱼(Trachurus murphyi)异交雌鱼的ZW性别决定系统和推测的性染色体。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-19 DOI: 10.1111/1755-0998.70034
C B Canales-Aguirre, S Ferrada-Fuentes, V Herrera-Yañez, Felipe Aguilera, Cristian Araya-Jaime, Natalia Lam, R Galleguillos
{"title":"Heterogametic Females Reveal a ZW Sex Determination System and a Putative Sex Chromosome for the Chilean Jack Mackerel, Trachurus murphyi.","authors":"C B Canales-Aguirre, S Ferrada-Fuentes, V Herrera-Yañez, Felipe Aguilera, Cristian Araya-Jaime, Natalia Lam, R Galleguillos","doi":"10.1111/1755-0998.70034","DOIUrl":"10.1111/1755-0998.70034","url":null,"abstract":"<p><p>Sex determination is the establishment of an organism's sex, usually by the inheritance at the fertilisation of certain genes present in sex chromosomes. However, this process is not universal, and indeed, sex might be determined through different factors, including genetic, environmental, behavioural, physiological or the interplay among them. Identification of the sex determination system, sex chromosomes and sex-linked markers is essential for understanding the genetics of sex determination in non-model organisms, which in turn can be used for several applications such as conservation and management. In fish, sex determination is a very flexible process and varies considerably among genera and families; even within individuals, it is subjected to modification by external factors. Here we report the discovery of the sex determination system, sex-linked loci and a putative sex chromosome for the Chilean jack mackerel Trachurus murphyi. Using a genome-wide approach, we identified 20 high-confidence sex-linked loci and found that females are heterogametic while males are homogametic, thus supporting a ZZ/ZW sex-determination system. All high-confidence sex-linked loci appear gametologous loci and are mapped in chromosome 13 of T. trachurus, a closely related species of T. murphyi. The female-to-male depth ratio analysis showed that most loci with a ratio close to 0.5 are located on this chromosome. Additionally, we generated a small GTseq panel that includes 13 loci supporting sex identification in individuals. The sexually identified chromosome has a strong effect on the population genetics analyses revealed by principal component analyses and F<sub>ST</sub> statistics. Our results indicate that T. murphyi shows a ZW sex-determination system and that chromosome 13 might be a sex chromosome, likely a Z chromosome. Altogether, our results provide new insights into sex determination systems in T. murphyi and T. trachurus and also constitute a new genomic resource for future applications in the conservation and management of these two economically relevant jack mackerel species.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70034"},"PeriodicalIF":5.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870588","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
Refining Zooplankton Diet Composition Studies Over Short and Long Time Scales by Combining 18S Metabarcoding With Fatty Acid Analyses. 结合18S元条形码和脂肪酸分析,改进浮游动物饮食组成在短期和长期尺度上的研究。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-18 DOI: 10.1111/1755-0998.70030
Nora-Charlotte Pauli, Katja Metfies, Stefan Neuhaus, Martin Graeve, Alison C Cleary, Morten H Iversen, Bettina Meyer
{"title":"Refining Zooplankton Diet Composition Studies Over Short and Long Time Scales by Combining 18S Metabarcoding With Fatty Acid Analyses.","authors":"Nora-Charlotte Pauli, Katja Metfies, Stefan Neuhaus, Martin Graeve, Alison C Cleary, Morten H Iversen, Bettina Meyer","doi":"10.1111/1755-0998.70030","DOIUrl":"https://doi.org/10.1111/1755-0998.70030","url":null,"abstract":"<p><p>Understanding diet composition is essential for unravelling trophic interactions in aquatic ecosystems. DNA metabarcoding, utilising various variable regions of the 18S rRNA gene, is increasingly employed to investigate zooplankton diet composition. However, accurate results depend on rapid inactivation of digestive enzymes and DNA nucleases through proper sample processing and preservation. In this study, we compare the prey communities of Antarctic krill retrieved from the 18S variable regions V4 and V7 and assess how different processing treatments affect the detected prey composition of both krill and salps. Our findings highlight the critical importance of prompt sample processing for species with highly efficient digestive enzymes, such as krill, to preserve rapidly digested prey, including gelatinous plankton. Comparative analyses of the V4 and V7 regions revealed significantly different prey communities within the same krill samples, indicating that these regions may not be suitable for direct comparisons within or across studies. To complement molecular approaches, we also analyse fatty acids (FA) as trophic markers which provide insights into dietary habits over both short and long time scales. By comparing FA signals from stomach and tissue samples of the same krill and salp individuals, we identified significant differences in trophic markers representing different plankton groups. These findings emphasise the necessity of separating digestive tract from tissue to distinguish between short- and long-term diet signals. Furthermore, integrating FA analysis with metabarcoding offers valuable insights into zooplankton digestion efficiency across taxonomic levels. This combined approach enhances our understanding of zooplankton feeding ecology and trophic interactions in marine ecosystems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70030"},"PeriodicalIF":5.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870589","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
DeepKin: Predicting Relatedness From Low-Coverage Genomes and Palaeogenomes With Convolutional Neural Networks. DeepKin:用卷积神经网络预测低覆盖率基因组和古基因组的相关性。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-18 DOI: 10.1111/1755-0998.70032
Merve N Güler, Ardan Yılmaz, Büşra Katırcıoğlu, Sarp Kantar, Tara Ekin Ünver, Kıvılcım Başak Vural, N Ezgi Altınışık, Emre Akbas, Mehmet Somel
{"title":"DeepKin: Predicting Relatedness From Low-Coverage Genomes and Palaeogenomes With Convolutional Neural Networks.","authors":"Merve N Güler, Ardan Yılmaz, Büşra Katırcıoğlu, Sarp Kantar, Tara Ekin Ünver, Kıvılcım Başak Vural, N Ezgi Altınışık, Emre Akbas, Mehmet Somel","doi":"10.1111/1755-0998.70032","DOIUrl":"https://doi.org/10.1111/1755-0998.70032","url":null,"abstract":"<p><p>DeepKin is a novel tool designed to predict relatedness from genomic data using convolutional neural networks (CNNs). Traditional methods for estimating relatedness often struggle when genomic data is limited, as with palaeogenomes and degraded forensic samples. DeepKin addresses this challenge by leveraging two CNN models, which are trained solely on simulated genomic data, to classify relatedness up to the third degree and to identify parent-offspring and sibling pairs. Our benchmarking shows DeepKin performs comparably or better than the widely used tool READv2. We validated DeepKin, which uses PLINK's .map and .ped files as input, on empirical palaeogenomes from three archaeological sites, demonstrating its robustness and adaptability across different genetic backgrounds, with accuracy > 90% above 10 K shared SNPs. By capturing information across genomic segments, DeepKin offers a new methodological path for relatedness estimation in settings with highly degraded samples, with applications in ancient DNA, as well as forensic and conservation genetics.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70032"},"PeriodicalIF":5.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870587","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
Comparative Decay Dynamics and Detectability of eDNA and eRNA in Connected and Isolated Freshwater Mesocosms Using Digital PCR. 利用数字PCR比较连接和分离的淡水中游生物中eDNA和eRNA的衰减动力学和可检测性。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-13 DOI: 10.1111/1755-0998.70028
Wendy B Morgado-Gamero, Orianne Tournayre, Melania E Cristescu
{"title":"Comparative Decay Dynamics and Detectability of eDNA and eRNA in Connected and Isolated Freshwater Mesocosms Using Digital PCR.","authors":"Wendy B Morgado-Gamero, Orianne Tournayre, Melania E Cristescu","doi":"10.1111/1755-0998.70028","DOIUrl":"https://doi.org/10.1111/1755-0998.70028","url":null,"abstract":"<p><p>Efficient use of environmental nucleic acids (eNAs) in freshwater biodiversity monitoring requires understanding their degradation and detectability in interconnected ecosystems. We employed a novel field-scale assay to compare environmental DNA (eDNA) and environmental RNA (eRNA) decay rates and detectability across four genetic markers (16S, 18S, COI and LDHA) in connected and isolated 1000-L mesocosms containing natural planktonic assemblages. This design provides ecologically relevant and complex settings to assess how connectivity influences the detectability of eNA over time. Isolated and head mesocosms were spiked with eNAs from cultured Daphnia pulex, absent from the water source, while downstream mesocosms received eNAs via unidirectional water transfers. Using digital PCR (dPCR), we captured fine-scale temporal patterns across mitochondrial and nuclear markers and transcript types (mRNA and rRNA), an approach rarely combined in previous research. eRNA degraded significantly faster than eDNA across markers and mesocosm types. Among RNA types, mRNA (COI, LDHA) degraded faster than rRNA (16S, 18S). eRNA followed a uniform monophasic decay pattern, whereas eDNA displayed biphasic decay for nuclear markers and monophasic decay for mitochondrial markers. eNA decay rates in this field-relevant mesocosm network exceeded those from laboratory scale. While decay rates remained consistent across networks, detectability declined with dilution. Even after a 10,000-fold dilution, both eNAs were detected in terminal mesocosms, demonstrating effective transport across the network. Although RNA degrades rapidly, high detectability was achieved across diverse dilutions using dPCR, highlighting eRNA's potential for detecting active biological communities in freshwater systems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70028"},"PeriodicalIF":5.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833545","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
Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species. 揭开生命之网:不完全谱系分选和杂交是梨物种多倍体化进化动力学的主要机制。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-12 DOI: 10.1111/1755-0998.70029
Ze-Tao Jin, Xiao-Hua Lin, Dai-Kun Ma, Si-Yu Xie, Jia-Xin Huang, Chen Ren, Liang Zhao, Lei Duan, Chao Xu, Richard G J Hodel, Jun Wu, Bin-Bin Liu
{"title":"Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species.","authors":"Ze-Tao Jin, Xiao-Hua Lin, Dai-Kun Ma, Si-Yu Xie, Jia-Xin Huang, Chen Ren, Liang Zhao, Lei Duan, Chao Xu, Richard G J Hodel, Jun Wu, Bin-Bin Liu","doi":"10.1111/1755-0998.70029","DOIUrl":"https://doi.org/10.1111/1755-0998.70029","url":null,"abstract":"<p><p>The traditional Tree of Life (ToL) model is increasingly challenged by the Web of Life (WoL) paradigm, which offers a more accurate depiction of organismal phylogeny, particularly in light of the incongruences often observed between gene and species trees. However, the absence of a standardised method for resolving evolutionary mechanisms - such as Incomplete Lineage Sorting (ILS), hybridisation, introgression, polyploidisation, and whole-genome duplication - remains a significant obstacle in defining the WoL. Characterised by extensive hybridisation events, the pear genus Pyrus provides an ideal model for exploring these complexities. In this study, we present a Step-by-Step Exclusion (SSE) approach for investigating the evolutionary pathways of Pyrus, based on Whole Genome Sequencing (WGS) and Deep Genome Skimming (DGS) data, and our results demonstrate that: (1) ILS, rather than polyploidisation, plays a dominant role in the origination of Pyrus; (2) the two subgenera of Pyrus followed independent evolutionary paths, influenced by geographical barriers formed through the uplift of the Tibetan Plateau and increased aridity in Central Asia; (3) both ILS and hybridisation have driven the diversification of subg. Pashia, while hybridisation alone has shaped the reticulate evolution of subg. Pyrus; (4) the establishment of the Silk Road during the Han Dynasty facilitated genetic exchange between subg. Pyrus and subg. Pashia. The SSE approach offers a versatile framework for studying the evolutionary mechanisms underlying the WoL paradigm.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70029"},"PeriodicalIF":5.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833567","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
High Imputation Accuracy Can Be Achieved Using a Small Reference Panel in a Natural Population With Low Genetic Diversity. 在遗传多样性较低的自然种群中,使用一个小的参考群体可以获得较高的输入精度。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-12 DOI: 10.1111/1755-0998.70024
Hui Zhen Tan, Katarina C Stuart, Tram Vi, Annabel Whibley, Sarah Bailey, Patricia Brekke, Anna W Santure
{"title":"High Imputation Accuracy Can Be Achieved Using a Small Reference Panel in a Natural Population With Low Genetic Diversity.","authors":"Hui Zhen Tan, Katarina C Stuart, Tram Vi, Annabel Whibley, Sarah Bailey, Patricia Brekke, Anna W Santure","doi":"10.1111/1755-0998.70024","DOIUrl":"https://doi.org/10.1111/1755-0998.70024","url":null,"abstract":"<p><p>Genotype imputation, the inference of missing genotypes using a reference set of population haplotypes, is a cost-effective tool for improving the quality and quantity of genetic datasets. Imputation is usually applied to large and well-characterised datasets of humans and livestock, even though it could also benefit smaller natural populations. This study aims to understand the best practices and effectiveness of imputation with a small reference panel for species with low genetic diversity, using a case study of a population of the hihi/stitchbird (Notiomystis cincta). We used a leave-one-out method to test imputation on 30 high-coverage hihi individuals where SNPs were masked before being imputed with Beagle v5.4. Imputation accuracy was measured using r<sup>2</sup>, the correlation between imputed and ground truth genotype dosages. We tested combinations of five imputation parameters, the inclusion of two linkage maps, reference panels of different sizes and compositions and targets of various SNP densities and sporadic missingness. We achieved mean r<sup>2</sup> exceeding 0.95 in most tests from a small reference panel of high-fecundity individuals. Imputation accuracy was not improved by including a linkage map and decreased at very low SNP densities. Imputed SNPs were filtered using r<sup>2</sup> to assess downstream heterozygosity calculations, the site frequency spectrum (SFS) and inference of runs of homozygosity (ROHs). We found that filtering and SNP density greatly affected heterozygosity and SFS at low SNP densities but that ROH inference was relatively robust to both. We provide a template for testing and optimising imputation in other wild populations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70024"},"PeriodicalIF":5.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833546","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
The CODEX Approach: High-Throughput Sequencing of the Cox-1 Barcode Fragment in Neogastropods (Mollusca, Gastropoda). CODEX方法:新腹足动物(软体动物,腹足动物)Cox-1条形码片段的高通量测序。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-11 DOI: 10.1111/1755-0998.70031
Nicolas Puillandre, Dario Zuccon, Jawad Abdelkrim, Thomas Lemarcis, Claudia Ratti, Mélanie Van Weddingen, Paul Zaharias, Sarah Farhat
{"title":"The CODEX Approach: High-Throughput Sequencing of the Cox-1 Barcode Fragment in Neogastropods (Mollusca, Gastropoda).","authors":"Nicolas Puillandre, Dario Zuccon, Jawad Abdelkrim, Thomas Lemarcis, Claudia Ratti, Mélanie Van Weddingen, Paul Zaharias, Sarah Farhat","doi":"10.1111/1755-0998.70031","DOIUrl":"https://doi.org/10.1111/1755-0998.70031","url":null,"abstract":"<p><p>DNA barcoding traditionally relies on Sanger sequencing but faces limitations with degraded samples. High-throughput sequencing (HTS) offers a cost-effective alternative, enabling rapid barcode generation for extensive datasets. The advantage of HTS is its ability to employ multiplexing strategies, allowing thousands of samples to be processed simultaneously in a single sequencing run. This study presents the CODEX approach, a double-indexed HTS method designed to sequence overlapping cox-1 barcode fragments, suitable for samples with degraded DNA. The approach was applied to neogastropods, a diverse lineage of marine molluscs, using specimens (both recently collected and relatively older) from the Muséum national d'Histoire naturelle (MNHN) collections. The pipeline was used to process 15,076 samples, yielding 10,905 cleaned and assembled sequences, achieving a success rate of 72.33%. The CODEX method demonstrated advantages over Sanger sequencing by enabling the recovery of barcodes from samples previously deemed unsuitable, with significantly reduced costs (€0.5 per sequence vs. €4.5). Notably, DNA quality and sequencing success were strongly correlated with collection date, emphasising the impact of preservation methods and storage conditions. Sequencing success rates varied among families but were not correlated with phylogenetic relationships or specimen size, indicating the robustness of the primers designed for neogastropods. This study highlights the efficiency of the CODEX approach for large-scale DNA barcoding projects, especially when handling degraded samples. The CODEX pipeline and associated resources are publicly accessible, offering a scalable solution for molecular systematics and beyond.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70031"},"PeriodicalIF":5.5,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815423","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
Test Species Discrimination in Codonopsis (Campanulaceae) Using Genome Skimming Data. 利用基因组略读数据测试党参属植物的物种区分。
IF 5.5 1区 生物学
Molecular Ecology Resources Pub Date : 2025-08-08 DOI: 10.1111/1755-0998.70025
Chun-Jiao Li, Yin-Zi Jiang, De-Zhu Li, Qing-Zhe Wu
{"title":"Test Species Discrimination in Codonopsis (Campanulaceae) Using Genome Skimming Data.","authors":"Chun-Jiao Li, Yin-Zi Jiang, De-Zhu Li, Qing-Zhe Wu","doi":"10.1111/1755-0998.70025","DOIUrl":"https://doi.org/10.1111/1755-0998.70025","url":null,"abstract":"<p><p>To overcome the limitations of conventional barcoding loci, plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences recovered from genome skimming, proposed as 'super-barcodes' have been suggested as candidates for delimitating recently diverged species or complex plant groups. DNA super-barcodes must be further assessed for their effectiveness in other diverse plant groups. This research focused on the genus Codonopsis, a medicinally significant yet taxonomically complex group characterised by morphological similarity and high phenotypic plasticity in response to environmental conditions. We analysed standard DNA barcodes and super-barcodes across 81 individuals from 36 of the 42 species of Codonopsis from Asia. Our work provides a comprehensive DNA barcode library for Codonopsis species identification. Our findings demonstrated that super-barcodes significantly improved the phylogenetic resolution and the discriminatory power compared to standard DNA barcodes. Since mitochondrial sequence variation is generally low in plant species, few studies have assessed its effectiveness as super-barcodes. We screened the mitochondrial protein-coding sequences (CDS) using genome skimming and evaluated the identification capacity of their combination. Unexpectedly, the discriminatory power of mitochondrial DNA with high nucleotide variation was comparable to that of the concatenated plastid CDS. However, the organelle genome cannot wholly determine the species boundaries of Codonopsis, which might be related to their rapid evolutionary radiation, ILS, hybridisation and strong natural selection. Future multi-locus nuclear markers will likely be developed in plants for additional discriminatory power. Our study provides new knowledge and insights into species discrimination of recently evolved Codonopsis taxa in a biodiversity hotspot.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70025"},"PeriodicalIF":5.5,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803029","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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