Molecular Ecology Resources最新文献_第6页

Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes 从环境微真核细胞中获取ASV解析rRNA操作子的长线程测序策略基准。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-07-09 DOI: 10.1111/1755-0998.13991

Christina Karmisholt Overgaard, Mahwash Jamy, Simona Radutoiu, Fabien Burki, Morten Kam Dahl Dueholm

{"title":"Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes","authors":"Christina Karmisholt Overgaard, Mahwash Jamy, Simona Radutoiu, Fabien Burki, Morten Kam Dahl Dueholm","doi":"10.1111/1755-0998.13991","DOIUrl":"10.1111/1755-0998.13991","url":null,"abstract":"The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13991","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141557577","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

Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration 下一代生物信息学：用于系统发生组数据探索的超快和用户友好型工具。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-07-06 DOI: 10.1111/1755-0998.13993

Kin Onn Chan

{"title":"Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration","authors":"Kin Onn Chan","doi":"10.1111/1755-0998.13993","DOIUrl":"10.1111/1755-0998.13993","url":null,"abstract":"With increasingly large genomic datasets, even routine bioinformatic tasks can be arduous, computationally demanding, and time-consuming. Additionally, most bioinformatic programs do not have a graphical user interface (GUI) and thus, require users to be minimally competent in command-line. These impediments present significant economic and technological barriers for practitioners who do not have access to advanced computational resources and support. In this issue of Molecular Ecology Resources, Handika and Esselstyn (2024) developed an ultrafast and memory-efficient bioinformatic tool, SEGUL, that performs common manipulations and calculations of summary statistics on phylogenomic datasets. SEGUL has two main features that distinguish it from other bioinformatic programs: (1) it is based on the recently emergent, high-performance programming language Rust, and (2) it has a GUI written using Flutter, a cross-platform programming framework that also supports mobile operating systems (mobile iOS, iPadOS and Android). By leveraging and combining the power of Rust and Flutter, SEGUL achieves significantly faster computation times and lower memory usage across different platforms and CPU architectures compared to similar programs. The unique and innovative features of SEGUL pave the way for a new era of bioinformatics that can be more energy-efficient, inclusive, and available to a broader swathe of users.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 7","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544221","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

Missing genotype imputation in non-model species using self-organizing maps. 利用自组织图对非模式物种中的缺失基因型进行估算。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-07-06 DOI: 10.1111/1755-0998.13992

Fernando Mora-Márquez, Juan Carlos Nuño, Álvaro Soto, Unai López de Heredia

{"title":"Missing genotype imputation in non-model species using self-organizing maps.","authors":"Fernando Mora-Márquez, Juan Carlos Nuño, Álvaro Soto, Unai López de Heredia","doi":"10.1111/1755-0998.13992","DOIUrl":"https://doi.org/10.1111/1755-0998.13992","url":null,"abstract":"Current methodologies of genome-wide single-nucleotide polymorphism (SNP) genotyping produce large amounts of missing data that may affect statistical inference and bias the outcome of experiments. Genotype imputation is routinely used in well-studied species to buffer the impact in downstream analysis, and several algorithms are available to fill in missing genotypes. The lack of reference haplotype panels precludes the use of these methods in genomic studies on non-model organisms. As an alternative, machine learning algorithms are employed to explore the genotype data and to estimate the missing genotypes. Here, we propose an imputation method based on self-organizing maps (SOM), a widely used neural networks formed by spatially distributed neurons that cluster similar inputs into close neurons. The method explores genotype datasets to select SNP loci to build binary vectors from the genotypes, and initializes and trains neural networks for each query missing SNP genotype. The SOM-derived clustering is then used to impute the best genotype. To automate the imputation process, we have implemented gtImputation, an open-source application programmed in Python3 and with a user-friendly GUI to facilitate the whole process. The method performance was validated by comparing its accuracy, precision and sensitivity on several benchmark genotype datasets with other available imputation algorithms. Our approach produced highly accurate and precise genotype imputations even for SNPs with alleles at low frequency and outperformed other algorithms, especially for datasets from mixed populations with unrelated individuals.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e13992"},"PeriodicalIF":5.5,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544220","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 a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies 迈向 DNA 条形码的美好未来：利用达西尼果蝇的 COI 基因片段评估基于单系和距离的物种鉴定。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-07-02 DOI: 10.1111/1755-0998.13987

Camiel Doorenweerd, Michael San Jose, Luc Leblanc, Norman Barr, Scott M. Geib, Arthur Y. C. Chung, Julian R. Dupuis, Arni Ekayanti, Elaida Fiegalan, Kennantudawage S. Hemachandra, Mohammad Aftab Hossain, Chia-Lung Huang, Yu-Feng Hsu, Kimberly Y. Morris, Andi Maryani A. Mustapeng, Jerome Niogret, Thai Hong Pham, Nhien Thi Nguyen, Uda G. A. I. Sirisena, Terrence Todd, Daniel Rubinoff

{"title":"Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies","authors":"Camiel Doorenweerd, Michael San Jose, Luc Leblanc, Norman Barr, Scott M. Geib, Arthur Y. C. Chung, Julian R. Dupuis, Arni Ekayanti, Elaida Fiegalan, Kennantudawage S. Hemachandra, Mohammad Aftab Hossain, Chia-Lung Huang, Yu-Feng Hsu, Kimberly Y. Morris, Andi Maryani A. Mustapeng, Jerome Niogret, Thai Hong Pham, Nhien Thi Nguyen, Uda G. A. I. Sirisena, Terrence Todd, Daniel Rubinoff","doi":"10.1111/1755-0998.13987","DOIUrl":"10.1111/1755-0998.13987","url":null,"abstract":"The utility of a universal DNA ‘barcode’ fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a ‘soft’ barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490259","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 Primula edelbergii S-locus is an example of a jumping supergene Primula edelbergii S-locus是跳跃超级基因的一个例子。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-06-30 DOI: 10.1111/1755-0998.13988

Giacomo Potente, Narjes Yousefi, Barbara Keller, Emiliano Mora-Carrera, Péter Szövényi, Elena Conti

{"title":"The Primula edelbergii S-locus is an example of a jumping supergene","authors":"Giacomo Potente, Narjes Yousefi, Barbara Keller, Emiliano Mora-Carrera, Péter Szövényi, Elena Conti","doi":"10.1111/1755-0998.13988","DOIUrl":"10.1111/1755-0998.13988","url":null,"abstract":"Research on supergenes, non-recombining genomic regions housing tightly linked genes that control complex phenotypes, has recently gained prominence in genomics. Heterostyly, a floral heteromorphism promoting outcrossing in several angiosperm families, is controlled by the S-locus supergene. The S-locus has been studied primarily in closely related Primula species and, more recently, in other groups that independently evolved heterostyly. However, it remains unknown whether genetic architecture and composition of the S-locus are maintained among species that share a common origin of heterostyly and subsequently diverged across larger time scales. To address this research gap, we present a chromosome-scale genome assembly of Primula edelbergii, a species that shares the same origin of heterostyly with Primula veris (whose S-locus has been characterized) but diverged from it 18 million years ago. Comparative genomic analyses between these two species allowed us to show, for the first time, that the S-locus can ‘jump’ (i.e. translocate) between chromosomes maintaining its function in controlling heterostyly. Additionally, we found that four S-locus genes were conserved but reshuffled within the supergene, seemingly without affecting their expression, thus we could not detect changes explaining the lack of self-incompatibility in P. edelbergii. Furthermore, we confirmed that the S-locus is not undergoing genetic degeneration. Finally, we investigated P. edelbergii evolutionary history within Ericales in terms of whole genome duplications and transposable element accumulation. In summary, our work provides a valuable resource for comparative analyses aimed at investigating the genetics of heterostyly and the pivotal role of supergenes in shaping the evolution of complex phenotypes.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13988","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464666","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

Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation Coryphaenoides yaquinae 的基因组测序揭示了深海适应性的趋同和特定世系的分子进化。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-06-30 DOI: 10.1111/1755-0998.13989

Wenhao Li, Jie Song, Huaming Tu, Shouwen Jiang, Binbin Pan, Jiazhen Li, Yongpeng Zhao, Liangbiao Chen, Qianghua Xu

{"title":"Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation","authors":"Wenhao Li, Jie Song, Huaming Tu, Shouwen Jiang, Binbin Pan, Jiazhen Li, Yongpeng Zhao, Liangbiao Chen, Qianghua Xu","doi":"10.1111/1755-0998.13989","DOIUrl":"10.1111/1755-0998.13989","url":null,"abstract":"Abyssal (3501–6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464665","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

Testing the applicability of environmental DNA metabarcoding to landscape genetics 测试环境 DNA 代谢编码对景观遗传学的适用性。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-06-24 DOI: 10.1111/1755-0998.13990

Souta Nakajima, Kenji Tsuri

{"title":"Testing the applicability of environmental DNA metabarcoding to landscape genetics","authors":"Souta Nakajima, Kenji Tsuri","doi":"10.1111/1755-0998.13990","DOIUrl":"10.1111/1755-0998.13990","url":null,"abstract":"Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D-loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue-based approaches by the same D-loop region and genome-wide SNP data. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA- and tissue-based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when comparing both in the D-loop region. The removal of low-frequency reads or the conversion to semi-quantitative rankings of eDNA data did not alter the correlation of genetic diversity and differentiation statistics with tissue-based approaches much. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation-by-distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454248","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

Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids 兰科-205：用于研究陆生兰花的进化、系统学和贸易的新的全基因组定制诱饵集。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-06-20 DOI: 10.1111/1755-0998.13986

Margaretha A. Veltman, Bastien Anthoons, Audun Schrøder-Nielsen, Barbara Gravendeel, Hugo J. de Boer

{"title":"Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids","authors":"Margaretha A. Veltman, Bastien Anthoons, Audun Schrøder-Nielsen, Barbara Gravendeel, Hugo J. de Boer","doi":"10.1111/1755-0998.13986","DOIUrl":"10.1111/1755-0998.13986","url":null,"abstract":"Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called ‘salep’. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13986","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425907","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

SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering SLRfinder：利用连锁不平衡聚类检测候选性连锁区域的方法。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-06-08 DOI: 10.1111/1755-0998.13985

Xueling Yi, Petri Kemppainen, Juha Merilä

{"title":"SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering","authors":"Xueling Yi, Petri Kemppainen, Juha Merilä","doi":"10.1111/1755-0998.13985","DOIUrl":"10.1111/1755-0998.13985","url":null,"abstract":"Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13985","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141287480","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

Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada 优化综合生物警戒工具箱，研究空气中霉菌生物群的空间分布和动态变化，重点是加拿大西部的谷物锈病真菌。

IF 5.5 1区生物学

Molecular Ecology Resources Pub Date : 2024-06-06 DOI: 10.1111/1755-0998.13983

Wen Chen, Nathaniel Newlands, Sarah Hambleton, André Laroche, Seyyed Mohammadreza Davoodi, Guus Bakkeren

{"title":"Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada","authors":"Wen Chen, Nathaniel Newlands, Sarah Hambleton, André Laroche, Seyyed Mohammadreza Davoodi, Guus Bakkeren","doi":"10.1111/1755-0998.13983","DOIUrl":"10.1111/1755-0998.13983","url":null,"abstract":"In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015–2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real-time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land-use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early-warning system for farmers to detect and mitigate impending disease outbreaks.","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13983","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141260073","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