Molecular Ecology Resources最新文献

{"title":"Editorial 2025","authors":"Shawn Narum, Joanna Kelley, Ben Sibbett","doi":"10.1111/1755-0998.14051","DOIUrl":"10.1111/1755-0998.14051","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826826","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":"Hīkina te mānuka: Advancing Indigenous Leadership in Molecular Ecology","authors":"Seafha C. Ramos, Andrew P. Kinziger, Alana Alexander","doi":"10.1111/1755-0998.14049","DOIUrl":"10.1111/1755-0998.14049","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 2","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764827","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 Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species","authors":"Ellie E. Armstrong,&nbsp;Chenyang Li,&nbsp;Michael G. Campana,&nbsp;Tessa Ferrari,&nbsp;Joanna L. Kelley,&nbsp;Dmitri A. Petrov,&nbsp;Katherine A. Solari,&nbsp;Jazlyn A. Mooney","doi":"10.1111/1755-0998.14048","DOIUrl":"10.1111/1755-0998.14048","url":null,"abstract":"<p>Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749503","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":"PhyloForge: Unifying Micro- and Macroevolution With Comprehensive Genomic Signals","authors":"Ya Wang,&nbsp;Wei Dong,&nbsp;Yufan Liang,&nbsp;Weiwei Lin,&nbsp;Junhao Chen,&nbsp;Robert Henry,&nbsp;Fei Chen","doi":"10.1111/1755-0998.14050","DOIUrl":"10.1111/1755-0998.14050","url":null,"abstract":"<div>\u0000 \u0000 <p>The dimensions of phylogenetic research have expanded to encompass the study of large-scale populations at the microevolutionary level and comparisons between different species or taxonomic units at the macroevolutionary level. Traditional phylogenetic tools often struggle to handle the diverse and complex data required for these different evolutionary scales. In response to this challenge, we introduce PhyloForge, a robust tool designed to seamlessly integrate the demands of both micro- and macroevolution, comprehensively utilising diverse phylogenomic signals, such as genes, SNPs, and structural variations, as well as mitochondrial and chloroplast genomes. PhyloForge's innovation lies in its capability to seamlessly integrate multiple phylogenomic signals, enabling the unified analysis of multidimensional genomic data. This unique feature empowers researchers to gain a more comprehensive understanding of diverse aspects of biological evolution. PhyloForge not only provides highly customisable analysis tools for experienced researchers but also features an intuitively designed interface, facilitating effortless phylogenetic analysis for beginners. Extensive testing across various domains, including animals, plants and fungi, attests to its broad applicability in the field of phylogenetics. In summary, PhyloForge has significant potential in the era of large-scale genomics, offering a new perspective and toolset for a deeper understanding of the evolution of life. PhyloForge codes could be found in GitHub (https://github.com/wangyayaya/PhyloForge/), and the program could be installed in Conda (https://anaconda.org/wangxiaobei/phyloforge).</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714806","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":"Temporal Variability in Effective Size (\u0000 \u0000 \u0000 \u0000 \u0000 N\u0000 ̂\u0000 \u0000 e\u0000 \u0000 \u0000 ) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance","authors":"Daniel E. Ruzzante,&nbsp;Gregory R. McCracken,&nbsp;Dylan J. Fraser,&nbsp;John MacMillan,&nbsp;Colin Buhariwalla,&nbsp;Joanna Mills Flemming","doi":"10.1111/1755-0998.14047","DOIUrl":"10.1111/1755-0998.14047","url":null,"abstract":"&lt;p&gt;Although efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long-term population dynamics. Here we took advantage of a rich dataset of seven brook trout (&lt;i&gt;Salvelinus fontinalis&lt;/i&gt;) populations, 5 consecutive years and 5400 individuals genotyped at 33 microsatellites to examine variation in estimates of effective and census size and in their ratio. We first estimated the annual effective number of breeders (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mover&gt;\u0000 &lt;mi&gt;N&lt;/mi&gt;\u0000 &lt;mo&gt;̂&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;&lt;sub&gt;&lt;i&gt;b&lt;/i&gt;&lt;/sub&gt;) using individuals aged 1+. We then adjusted these estimates using two life history traits, to obtain &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mover&gt;\u0000 &lt;mi&gt;N&lt;/mi&gt;\u0000 &lt;mo&gt;̂&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;b&lt;/mi&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;adj&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/mfenced&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; and subsequently, &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mover&gt;\u0000 &lt;mi&gt;N&lt;/mi&gt;\u0000 &lt;mo&gt;̂&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;e&lt;/mi&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;adj&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/mfenced&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; following Waples et al. (2013). &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mover&gt;\u0000 &lt;mi&gt;N&lt;/mi&gt;\u0000 &lt;mo&gt;̂&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;e&lt;/mi&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;adj&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/mfenced&gt;\u0000 ","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708718","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":"Chromosomal-Level Genome Suggests Adaptive Constraints Leading to the Historical Population Decline in an Extremely Endangered Plant","authors":"Shao Shao,&nbsp;Yulong Li,&nbsp;Xiao Feng,&nbsp;Chuanfeng Jin,&nbsp;Min Liu,&nbsp;Ranran Zhu,&nbsp;Miles E. Tracy,&nbsp;Zixiao Guo,&nbsp;Ziwen He,&nbsp;Suhua Shi,&nbsp;Shaohua Xu","doi":"10.1111/1755-0998.14045","DOIUrl":"10.1111/1755-0998.14045","url":null,"abstract":"<div>\u0000 \u0000 <p>Increased human activity and climate change have significantly impacted wild habitats and increased the number of endangered species. Exploring evolutionary history and predicting adaptive potential using genomic data will facilitate species conservation and biodiversity recovery. Here, we examined the genome evolution of a critically endangered tree <i>Pellacalyx yunnanensis</i>, a plant species with extremely small populations (PSESP) that is narrowly distributed in Xishuangbanna, China. The species has neared extinction due to economic exploitation in recent decades. We assembled a chromosome-level genome of 334 Mb, with the N50 length of 20.5 Mb. Using the genome, we discovered that <i>P. yunnanensis</i> has undergone several population size reductions, leading to excess deleterious mutations. The species may possess low adaptive potential due to reduced genetic diversity and the loss of stress-responsive genes. We estimate that <i>P. yunnanensis</i> is the basal species of its genus and diverged from its relatives during global cooling, suggesting it was stranded in unsuitable environments during periods of dramatic climate change. In particular, the loss of seed dormancy leads to germination under unfavourable conditions and reproduction challenges. This dormancy loss may have occurred through genetic changes that suppress ABA signalling and the loss of genes involved in seed maturation. The high-quality genome has also enabled us to reveal phenotypic trait evolution in Rhizophoraceae and identify divergent adaptation to intertidal and inland habitats. In summary, our study elucidates mechanisms underlying the decline and evaluates the adaptive potential of <i>P. yunnanensis</i> to future climate change, informing future conservation efforts.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685385","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":"Development of SNP Panels from Low-Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada","authors":"Anne Beemelmanns,&nbsp;Raphaël Bouchard,&nbsp;Sozos Michaelides,&nbsp;Eric Normandeau,&nbsp;Hyung-Bae Jeon,&nbsp;Badrouyk Chamlian,&nbsp;Charles Babin,&nbsp;Philippe Hénault,&nbsp;Océane Perrot,&nbsp;Les N. Harris,&nbsp;Xinhua Zhu,&nbsp;Dylan Fraser,&nbsp;Louis Bernatchez †,&nbsp;Jean-Sébastien Moore","doi":"10.1111/1755-0998.14040","DOIUrl":"10.1111/1755-0998.14040","url":null,"abstract":"<p>Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational and subsistence mixed-stock fisheries. Arctic Char (<i>Salvelinus alpinus</i>), Brook Trout (<i>Salvelinus fontinali</i>s) and Lake Whitefish (<i>Coregonus clupeaformis</i>) are among the most harvested and consumed fish species in Northern Indigenous communities in Canada, contributing significantly to food security, culture, tradition and economy. However, genetic resources supporting Indigenous fisheries have not been widely accessible to northern communities (e.g. Inuit, Cree, Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses of three salmonids, to support fisheries stewardship or co-management in Northern Canada. Using low-coverage Whole Genome Sequencing data from 418 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec) and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were then used to design GT-seq panels, thus enabling high-throughput genotyping for these species. The three GT-seq panels yielded an average of 413 autosomal loci and were validated using 525 individuals with an average assignment accuracy of 83%. Thus, these GT-seq panels are powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed-stock fisheries across multiple regions. Interweaving genomic data derived from these tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programmes and the economy in Northern Canada.</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/10.1111/1755-0998.14040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646387","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":"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}