Molecular Ecology Resources最新文献

{"title":"Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations","authors":"Satoshi Hiraoka,&nbsp;Minoru Ijichi,&nbsp;Hirohiko Takeshima,&nbsp;Yohei Kumagai,&nbsp;Ching-Chia Yang,&nbsp;Yoko Makabe-Kobayashi,&nbsp;Hideki Fukuda,&nbsp;Susumu Yoshizawa,&nbsp;Wataru Iwasaki,&nbsp;Kazuhiro Kogure,&nbsp;Takuhei Shiozaki","doi":"10.1111/1755-0998.14042","DOIUrl":"10.1111/1755-0998.14042","url":null,"abstract":"<p>The ammonia monooxygenase subunit A (<i>amoA</i>) gene has been used to investigate the phylogenetic diversity, spatial distribution and activity of ammonia-oxidising archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of <i>amoA</i> is a widely used method; however, it produces inaccurate results owing to the lack of a ‘universal’ primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low abundance of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realisable sequencing depth. In this study, we developed a probe set and bioinformatics workflow for <i>amoA</i> enrichment sequencing using a hybridisation capture technique. Using metagenomic mock community samples, our approach effectively enriched <i>amoA</i> genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or <i>amoA</i> gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 ± 27.2%) than for non-capture samples (0.05 ± 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646394","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":"HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors","authors":"Jiaying Li,&nbsp;Yuze Gao,&nbsp;Guocheng Shu,&nbsp;Xuanzhong Chen,&nbsp;Jiahao Zhu,&nbsp;Si Zheng,&nbsp;Ting Chen","doi":"10.1111/1755-0998.14046","DOIUrl":"10.1111/1755-0998.14046","url":null,"abstract":"<div>\u0000 \u0000 <p>Symbiotic microbiota strongly impact host physiology. Amphibians and reptiles occupy a pivotal role in the evolutionary history of Animalia, and they are of significant ecological, economic, and scientific value. Many prior studies have found that symbiotic microbiota in herpetofaunal species are closely associated with host phylogeny, physiological traits, and environmental factors; however, insufficient integrated databases hinder researchers from querying, accessing, and reanalyzing these resources. To rectify this, we built the first herpetofaunal microbiota database (HMicroDB; https://herpdb.com/) that integrates 11,697 microbiological samples from 337 host species (covering 23 body sites and associated with 23 host phenotypic or environmental factors), and we identified 11,084 microbial taxa by consistent annotation. The standardised analysis process, cross-dataset integration, user-friendly interface, and interactive visualisation make the HMicroDB a powerful resource for researchers to search, browse, and explore the relationships between symbiotic microbiota, hosts, and environment. This facilitates research in host–microbiota coevolution, biological conservation, and resource utilisation.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613334","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":"OGU: A Toolbox for Better Utilising Organelle Genomic Data","authors":"Ping Wu,&nbsp;Ningning Xue,&nbsp;Jie Yang,&nbsp;Qiang Zhang,&nbsp;Yuzhe Sun,&nbsp;Wen Zhang","doi":"10.1111/1755-0998.14044","DOIUrl":"10.1111/1755-0998.14044","url":null,"abstract":"<p>Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open-source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating and organising sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity. The primer module designs universal primers for downstream applications. Finally, a visualisation pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we identified 30 plastid intergenic spacers. These spacers exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, highlighting the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilisation of organelle genomic data and broaden the prospects for related research endeavours.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613338","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":"Correction to “Characterisation of Putative Circular Plasmids in Sponge-Associated Bacterial Communities Using a Selective Multiply-Primed Rolling Circle Amplification”","authors":"","doi":"10.1111/1755-0998.14043","DOIUrl":"10.1111/1755-0998.14043","url":null,"abstract":"<p>Oliveira, V., A. R. M. Polónia, D. F. R. Cleary, et al. 2021. “Characterization of putative circular plasmids in sponge-associated bacterial communities using a selective multiply-primed rolling circle amplification.” <i>Molecular Ecology Resources</i> <b>21</b>, no. 1: 110–121. https://doi.org/10.1111/1755-0998.13248.</p><p>The authors of the above article noticed an error in the DNA concentration which is detailed in the ‘Methods’ section, section 2.3 (‘Selective multiply-primed rolling circle amplification’), paragraph 2. The correct text should read as ‘1 μL template DNA (ca. 200 ng)’.</p><p>The authors apologise for this error and any inconvenience it may have caused.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567134","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":"The Chromosome-Scale Genome of Magnolia sieboldii K. Koch Provides Insight Into the Evolutionary Position of Magnoliids and Seed Germination","authors":"Xiujun Lu,&nbsp;Mei Mei,&nbsp;Lin Liu,&nbsp;Xin Xu,&nbsp;Wanfeng Ai","doi":"10.1111/1755-0998.14030","DOIUrl":"10.1111/1755-0998.14030","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Magnolia sieboldii</i> K. Koch (<i>M. sieboldii</i>) stands as an elegant tree species within the Magnoliaceae family, esteemed for its exquisite beauty, cultural significance and economic advantages. The species faces challenges in seed germination under natural conditions, primarily attributed to morphological dormancy. Despite its significance, the molecular mechanisms governing <i>M. sieboldii</i> seed germination remain elusive, compounded by the absence of genomic resources specific to this species. In this study, we present the first chromosome-scale genome assembly of <i>M. sieboldii</i>, with a total genome size of 2.01 Gb, including 1096 scaffolds assigned to 19 chromosomes (N50 = 102.4 Mb). Phylogenetic analyses, incorporating 13 plant species, illuminate the evolutionary independence of Magnoliids from monocots and eudicots, positioning them as a sister clade. Through RNA-seq analysis, we identify pivotal genes and pathways contributing to seed dormancy and germination. In addition, our investigation delves into the the far-red-impaired response (FAR1) transcription factor gene family, revealing their enrichment throughout evolution and their involvement in the intricate process of seed germination. This comprehensive genome sequencing initiative offers invaluable insights into the biological attributes of <i>M. sieboldii</i>, with a specific emphasis on unravelling the complexities of seed dormancy and germination.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542399","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":"A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections","authors":"Oliver W. White,&nbsp;Andie Hall,&nbsp;Ben W. Price,&nbsp;Suzanne T. Williams,&nbsp;Matthew D. Clark","doi":"10.1111/1755-0998.14036","DOIUrl":"10.1111/1755-0998.14036","url":null,"abstract":"<p>Low coverage ‘genome-skims’ are often used to assemble organelle genomes and ribosomal gene sequences for cost-effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction-based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome-skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines <i>skim2mito</i>, <i>skim2rrna</i> and <i>gene2phylo</i>, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, <i>skim2mito</i> and <i>skim2rrna</i> perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low-coverage genome skims. The third pipeline <i>gene2phylo</i> takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491750","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":"That's Not a Hybrid: How to Distinguish Patterns of Admixture and Isolation By Distance","authors":"Ben J. Wiens,&nbsp;Jocelyn P. Colella","doi":"10.1111/1755-0998.14039","DOIUrl":"10.1111/1755-0998.14039","url":null,"abstract":"<div>\u0000 \u0000 <p>Describing naturally occurring genetic variation is a fundamental goal of molecular phylogeography and population genetics. Popular methods for this task include <i>STRUCTURE</i>, a model-based algorithm that assigns individuals to genetic clusters, and principal component analysis (PCA), a parameter-free method. The ability of <i>STRUCTURE</i> to infer mixed ancestry makes it popular for documenting natural hybridisation, which is of considerable interest to evolutionary biologists, given that such systems provide a window into the speciation process. Yet, <i>STRUCTURE</i> can produce misleading results when its underlying assumptions are violated, like when genetic variation is distributed continuously across geographic space. To test the ability of <i>STRUCTURE</i> and PCA to accurately distinguish admixture from continuous variation, we use forward-time simulations to generate population genetic data under three demographic scenarios: two involving admixture and one with isolation by distance (IBD). <i>STRUCTURE</i> and PCA alone cannot distinguish admixture from IBD, but complementing these analyses with triangle plots, which visualise hybrid index against interclass heterozygosity, provides more accurate inference of demographic history, especially in cases of recent admixture. We demonstrate that triangle plots are robust to missing data, while <i>STRUCTURE</i> and PCA are not, and show that setting a low allele frequency difference threshold for ancestry-informative marker (AIM) identification can accurately characterise the relationship between hybrid index and interclass heterozygosity across demographic histories of admixture and range expansion. While <i>STRUCTURE</i> and PCA provide useful summaries of genetic variation, results should be paired with triangle plots before admixture is inferred.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520551","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":"Correcting for Replicated Genotypes May Introduce More Problems Than it Solves","authors":"Patrick G. Meirmans","doi":"10.1111/1755-0998.14041","DOIUrl":"10.1111/1755-0998.14041","url":null,"abstract":"<p>Across the tree of life, many organisms are able to reproduce clonally, via vegetative spread, budding or parthenogenesis. In population genetic analyses of clonally reproducing organisms, it is common practice to retain only a single representative per multilocus genotype. Though this practice of clone correction is widespread, the theoretical justification behind it has been very little studied. Here, I use individual-based simulations to study the effect of clone correction on the estimation of the genetic summary statistics <i>H</i>_O, <i>H</i>_S, <i>F</i>_IS, <i>F</i>_ST, <i>F</i>′′_ST and <i>D</i>_est. The simulations follow the standard finite island model, consisting of a set of populations connected by gene flow, but with a variable rate of sexual versus asexual reproduction. The results of the simulations show that by itself, the inclusion of replicated genotypes does not lead to a deviation in the values of the summary statistics, except when the rate of sexual reproduction is less than about one in thousand. However, clone correction can introduce a strong deviation in the values of most of the statistics, when compared to a scenario of full sexual reproduction. For <i>H</i>_S and <i>F</i>_IS, this deviation can be informative about the process of asexual reproduction, but for <i>F</i>_ST, <i>F</i>′′_ST and <i>D</i>_est, clone correction can lead to incorrect conclusions. I therefore argue that clone correction is not strictly necessary, but can in some cases be insightful. However, when clone correction is applied, it is imperative that results for both the corrected and uncorrected data are presented.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491751","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":"Detecting Assembly Errors With Klumpy: Building Confidence in Your Daily Genomic Analysis","authors":"Isheng Jason Tsai","doi":"10.1111/1755-0998.14037","DOIUrl":"10.1111/1755-0998.14037","url":null,"abstract":"<p>In the realm of genome assembly, even minor errors can send researchers down to rabbit holes of unintended misinterpretation. Enter Klumpy—a tool designed to help detecting these elusive mistakes before they cause significant problems. By providing detailed, region-specific assessments and an intuitive visualisation platform, Klumpy (Madrigal, et al. 2024) empowers researchers to pinpoint and resolve potential issues with precision, paving the way for more reliable downstream analyses and discoveries.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491752","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":"Genotyping Error Detection and Customised Filtration for SNP Datasets","authors":"Noa Yaffa Kan-Lingwood,&nbsp;Liran Sagi,&nbsp;Shahar Mazie,&nbsp;Naama Shahar,&nbsp;Lilith Zecherle Bitton,&nbsp;Alan Templeton,&nbsp;Daniel Rubenstein,&nbsp;Amos Bouskila,&nbsp;Shirli Bar-David","doi":"10.1111/1755-0998.14033","DOIUrl":"10.1111/1755-0998.14033","url":null,"abstract":"<div>\u0000 \u0000 <p>A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the ‘true’ genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non-invasive sampling from the Asiatic wild ass (<i>Equus hemionus</i>) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (<i>r</i>) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (<i>p</i> = 0.0002) and a significant increase in relatedness, from <i>r</i> = 0.98 to <i>r =</i> 0.991 (<i>p</i> = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142454253","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}