Molecular Ecology Resources最新文献

{"title":"Correction to “Complete Mitochondrial Genomes of Eleven Extinct or Possibly Extinct Bird Species”","authors":"","doi":"10.1111/1755-0998.70181","DOIUrl":"https://doi.org/10.1111/1755-0998.70181","url":null,"abstract":"<p>\u0000 <span>Anmarkrud, J. A.</span> and <span>J. T. Lifjeld</span>. <span>2017</span>. “ <span>Complete mitochondrial genomes of eleven extinct or possibly extinct bird species</span>.” <i>Molecular Ecology Resources</i> <span>17</span>, no. <span>2</span>: <span>334</span>–<span>341</span>.\u0000 </p><p>One of the sequenced specimens (Accession number: NHMO-BI-67809, Natural History Museum, University of Oslo) was wrongly identified as <i>Akialoa obscura</i>. The error was discovered during recent examination of the voucher specimen and its accession history. The correct species identification is <i>Akialoa stejnegeri</i>, an extinct species from the island of Kauai in Hawaii Islands, USA. The voucher specimen was part of one of two shipments of Hawaiian birds sent from a Norwegian collector, Valdemar Knudsen, in 1890 and 1893. Mr. Knudsen was a resident of Kauai Island.</p><p>To the best of our knowledge, this misidentification affects only the taxonomic assignment of that particular mitogenome and does not alter the sequence data, analytical procedures or the main conclusions of the study.</p><p>We thank Roland van der Vliet, Justin Jansen and Lars Erik Johannessen for bringing this misidentification to our attention.</p><p>We apologize for this error.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 6","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148647696","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":"Umbilical Cord: A Non-Invasive DNA Source for Sea Turtle Genomics","authors":"Gisela Marín-Capuz,&nbsp;Elena Abella,&nbsp;Marta Pascual,&nbsp;Cinta Pegueroles,&nbsp;Carlos Carreras","doi":"10.1111/1755-0998.70184","DOIUrl":"10.1111/1755-0998.70184","url":null,"abstract":"<p>High-throughput sequencing has revolutionised conservation genomics by enabling genome-wide information even in non-model species. However, obtaining non-invasive samples for genomics remains challenging in species like sea turtles, which spend most of their lives in the open ocean. In addition, traditional sampling methods are often impractical or unsafe for hatchlings, highlighting the need for alternative approaches. We investigated the potential of umbilical cords (UCs), both from the proximal and distal regions, as a non-invasive sampling method. We assessed the suitability of UC sampling by evaluating prevalence under different incubation conditions, and whether the UC reflected a genetic origin from the mother or offspring. We analysed 76 samples with 2bRAD from five Spanish loggerhead turtle (<i>Caretta caretta</i>) emerging nests, including UCs from 13 hatchlings (both proximal and distal region), 48 hatchling blood samples (four with genotyped UCs) and blood from two breeding females. Using the Percentage of Shared Genotypes (PSG) analysis, we determined that the UC genotype from both sides matched the hatchling blood genotype (97.7%), while PSG were lower between related individuals (73.5%) and even lower between unrelated individuals (56.5%). UC prevalence varied by incubation type, appearing in 100% of artificially incubated nests in Spain, in 25% of Spain's naturally incubated nests, an emergent nesting population, and in only 4.5% of nests naturally incubated in Cape Verde, an established nesting population. Our findings establish UCs as a reliable non-invasive DNA source for hatchlings, particularly in incubator-hatched eggs. This approach advances genomic analysis while minimising disturbance, offering insights into population genetics and conservation strategies.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 6","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70184","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148629024","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":"Unified Multi-Caller Ensemble (UME) Generates an Unbiased Maize Haplotype Map for Variable Coverage Whole Genome Data","authors":"Miguel Vallebueno-Estrada,&nbsp;Kelly Swarts","doi":"10.1111/1755-0998.70150","DOIUrl":"10.1111/1755-0998.70150","url":null,"abstract":"<p>We present a novel diversity-focused haplotype map (HapMap) that characterizes over 64.5 million maize (<i>Zea mays ssp. mays</i>) single nucleotide polymorphisms (SNPs) genotyped across 818 individuals from diverse backgrounds. This HapMap aims to balance the variation obtained from domesticated landraces and inbred lines, outgroup <i>Zea</i> spp. and more distant <i>Tripsacum</i> spp. in order to minimize ascertainment bias for diversity studies. Included individuals derive from public data from various experimental setups and coverages, which is challenging for standard SNP callers to accommodate. We provide evidence of coverage biases associated with standard callers that influence resulting variation and introduce a novel approach called Unified Multi-Caller Ensemble (UME), which enhances variant calling accuracy in low-coverage and mixed-coverage genomic datasets. UME corrects for coverage bias resulting from inter-sample coverage heterogeneity by leveraging evidence from variant callers with orthogonal strategies, re-calibrating the error probabilities across callers to minimize the impact of error biases inherent to a given caller. It outperforms individual strategies and excels in de novo variant calling, taking advantage of instances of higher depth reads, even in low coverage individuals, while preserving biologically informative variant relationships across coverage levels. An important feature of UME is the independence from population allele frequencies in the discovery panel, thus avoiding ascertainment bias resulting from unbalanced input genetic diversity. Discovered variants are less affected by ascertainment bias because no population filtering is used, and the full diversity of SNPs is retained in the final variant call set to maximize the utility of the dataset for production calling newly sequenced samples. We present a strategy for filtering the recalibrated error profiles that relies on maximizing demographic signals to retain genetic relationships within the population while reducing sequencing error. After the variant discovery phase, we employ the UME production stage, which enriches genotype calling across all coverage levels, benefiting low-coverage samples. Error introduced in this process is removed through subsequent filtering. Using this approach, we generated a coverage bias-controlled maize HapMap database, providing a comprehensive representation of maize accessions and emphasizing landrace diversity. This diverse panel of domesticated maize and outgroups from across the Americas enables accurate genotyping in low-coverage samples while offering crucial context for interpreting diversity, particularly for natural diversity and paleogenomic analyses.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148596888","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":"Operationalising Environmental DNA (eDNA) Detection of Major Malaria Vector Species in Ghana","authors":"Mojca Kristan,&nbsp;Yaw A. Afrane,&nbsp;Sophie Moss,&nbsp;Yaw Akuamoah-Boateng,&nbsp;Abdul Rahim Mohammed Sabtiu,&nbsp;Judith Dzifa Azumah,&nbsp;Anisa Abdulai,&nbsp;Isaac Kwame Sraku,&nbsp;Bright Churchill Obeng,&nbsp;Karen L. Figueroa Chilito,&nbsp;Jo Lines,&nbsp;Sian E. Clarke,&nbsp;Taane G. Clark,&nbsp;Susana Campino,&nbsp;Louisa A. Messenger","doi":"10.1111/1755-0998.70154","DOIUrl":"10.1111/1755-0998.70154","url":null,"abstract":"<p>The global landscape of vector-borne diseases (VBDs) is shifting, driven by climate change, urbanisation and widespread habitat modification, requiring novel approaches to surveillance, prevention and control. To improve our capacity to respond to real-time emergent VBD threats, this study undertook cross-sectional sampling of suspected mosquito breeding sites in Greater Accra and Western Region, Ghana, to assess the operational feasibility of environmental DNA (eDNA) detection of major malaria vector species. eDNA deposited by wild, immature <i>Anopheles gambiae</i> s.l., isolated from a 50 mL water sample, was detectable using both end-point PCR and qPCR, achieving high levels of sensitivity (76.28%) and specificity (100%). Furthermore, we recovered PCR amplicons covering eight known insecticide resistance mutations from eDNA collected in natural breeding sites. This study represents the first proof-of-concept demonstrating that eDNA can be used for the simultaneous identification of <i>Anopheles</i> vectors and circulating insecticide resistance alleles directly from aquatic habitats in the community, including the first report of the mutation <i>gste2</i>-F120L in Ghana. Our eDNA sampling methodology was designed for citizen scientists as end-point users. We recommend fixed, single-use filters for sampling 50 mL of water as a highly feasible, sensitive and specific, community-led mosquito vector surveillance tool, which requires minimal training or technical infrastructure.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70154","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148596854","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":"Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages","authors":"Irene Villa-Machío,&nbsp;Irene Masa-Iranzo,&nbsp;Nicolai M. Nürk,&nbsp;Lisa Pokorny,&nbsp;Andrea S. Meseguer","doi":"10.1111/1755-0998.70173","DOIUrl":"10.1111/1755-0998.70173","url":null,"abstract":"<p>The combination of target capture sequencing (TCS) with low-coverage whole genome sequencing (lcWGS), an approach known as Hyb-Seq, has allowed the integration of natural history collections into the genomics revolution, transforming biodiversity research. To implement Hyb-Seq, a collection of genomic targets is needed to design probes. In flowering plants, the Angiosperms353 kit has been proven effective at multiple evolutionary scales, with limitations. Malpighiales is one of the most challenging flowering plant orders to resolve. Within this order, the clusioid clade (~2.200 species, 94 genera, five families) is no exception. To resolve phylogenetic relationships in this recalcitrant clade, we design a custom probe set composed of 39,936 120-mer probes targeting 626 nuclear orthologs. The Clusioids626 kit includes all Angiosperms353 targets and 273 clusioid-specific ones, carefully chosen taking copy-number, length evenness, and phylogenetic informativeness into account. We tested our probe set on 70 accessions representing all clusioid families and tribes. On average, 50.4% reads mapped to our targets, recovering a median of ~600 orthologs/sample. Relationships for all clusioid families are fully resolved for our nuclear targets. A Hypericaceae-Podostemaceae clade is sister to Calophyllaceae, which are all sister to Bonnetiaceae, and then to Clusiaceae. Additionally, we retrieved 105 plastid coding sequences from the lcWGS fraction with a custom target file, evidencing strong incongruence between nuclear and plastid topologies. The Clusioids626 kit performs better than the Angiosperms353 one alone. Our design workflow can be extended to other lineages for which a universal probe set exists but more resolution is needed.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70173","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148596904","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":"Comparing Accuracy and Biases of DNA Metabarcoding, Hybridization Capture, and Metagenomic Sequencing for Quantifying Herbivore Diets","authors":"Charlotte E. Eriksson,&nbsp;Lisa Shipley,&nbsp;Darren A. Clark,&nbsp;Taal Levi","doi":"10.1111/1755-0998.70175","DOIUrl":"https://doi.org/10.1111/1755-0998.70175","url":null,"abstract":"<p>DNA metabarcoding using relative read abundance (RRA) is commonly applied to estimate herbivore diet composition, yet its quantitative accuracy remains uncertain. We assessed taxonomic resolution and quantitative performance of RRA from DNA metabarcoding compared to metagenomic sequencing and hybridization capture, using deer scats from feeding trials and recreated diet samples using plant tissues. All methods recovered plant composition in recreated diets (<i>R</i>² = 0.59–0.82), indicating accurate scaling with biomass in the absence of digestion, with only minor bias from amplicon length in DNA metabarcoding. In contrast, RRA from scat samples performed poorly (<i>R</i>² &lt; 0.01) across all methods largely due to differential plant digestibility. Correcting for digestibility, measured with acid detergent lignin and acid-insoluble ash, was strongly supported in mixed-effects models and improved prediction of dietary composition, although species-level variation remained. For metagenomic sequencing and hybridization capture, we also evaluated Relative Genome Coverage (RGC), a novel relative abundance metric quantifying the proportion of each plant's chloroplast genome covered by mapped reads, normalized for genome length. RGC further improved correlations in recreated diets (<i>R</i>² = 0.82–0.84) and, with hybridization capture, largely overcame digestibility-related biases in scat samples (<i>R</i>² = 0.57) without correction. When such corrections are infeasible, hybridization capture with uncorrected RGC may achieve higher quantitative accuracy in scat samples. Our results provide practical guidance for improving molecular herbivore diet analysis and highlight the importance of accounting for digestion-related biases.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70175","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467371","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":"Genome Assemblies for Seven Families of Birds From the Global South","authors":"K. L. Vinay,&nbsp;Naman Goyal,&nbsp;Ashwin Warudkar,&nbsp;Chiti Arvind,&nbsp;V. V. Robin","doi":"10.1111/1755-0998.70162","DOIUrl":"10.1111/1755-0998.70162","url":null,"abstract":"<p>Tropical regions are biodiversity-rich, yet remain underrepresented in the availability of genomic resources, as is evident in the Western Ghats of India, a biodiversity hotspot with high endemism. Here, we present high-quality, de novo genome assemblies for seven birds, representing seven families distributed in the Western Ghats: Black-naped Monarch (Monarchidae: <i>Hypothymis azurea</i>), Indian Yellow Tit (Paridae: <i>Machlolophus aplonotus</i>), Brown-cheeked Fulvetta (Leiothrichidae: <i>Alcippe poioicephala</i>), Malabar Trogon (Trogonidae: <i>Harpactes fasciatus</i>), Blue-bearded Bee-eater (Meropidae: <i>Nyctyornis athertoni</i>), Malabar Whistling-Thrush (Muscicapidae: <i>Myophonus horsfieldii</i>), Orange-headed Thrush (Turdidae: <i>Geokichla citrina</i>). Using a hybrid Oxford Nanopore long reads—Illumina short reads approach, we assembled genomes with sizes ranging from 1.03 to 1.13 Gbp. All assemblies demonstrated high contiguity and completeness (BUSCO scores &gt; 97%, UCEs &gt; 4799). Repeat masking identified ~10% of the genomes as interspersed repeats. Of the predicted protein-coding genes, an average of 9619 per species received high-confidence functional annotation hits. Comparative analysis showed our assemblies had significantly higher contiguity than the median of existing avian genomes on NCBI (Wilcoxon test, <i>p</i> = 0.00226). Our genome assemblies fill a key geographic and taxonomic gap in the genomic data and provide a foundational resource for evolutionary and ecological research in the Old-World tropics.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70162","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454059","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":"Phylogenetic Authentication of Amplicon Sequence Variants in Single-Specimen Metabarcoding of Tropical Insects","authors":"Sarawut Ounjai,&nbsp;Huaxi Liu,&nbsp;Zichen Zhou,&nbsp;Maria Pestana Correia,&nbsp;Thomas J. Creedy,&nbsp;Carmelo Andújar,&nbsp;Paula Arribas,&nbsp;Alfried P. Vogler","doi":"10.1111/1755-0998.70178","DOIUrl":"10.1111/1755-0998.70178","url":null,"abstract":"<p>High-throughput sequencing (HTS) allows large-scale DNA barcoding of individually tagged specimens (‘megabarcoding’), but deep amplicon sequencing produces a mixture of authentic mitochondrial sequences together with nuclear pseudogenes (NUMTs), environmental and cross-sample contaminants, and sequencing artefacts. Standard approaches relying on read clustering or dominant-read selection often fail to classify these types, leading to incorrect taxonomic identifications and species counts. We developed an authentication framework by integrating abundance filtering, phylogenetic placement and taxonomic congruence. The workflow was applied to 18,533 morphospecies of tropical beetles (Coleoptera) from multiple biogeographic regions, which were imaged for family-level identification, prior to individual Illumina barcoding. Sequencing yielded &gt; 36 million reads and 64,544 unique ASVs, which were evaluated against a reference phylogeny of &gt; 13,000 mitogenomes. Authentication succeeded for 86.5% of quality-passing specimens (15,901 ASVs). Non-authentic sequences were technical artefacts (58.0%), environmental contamination including prey DNA (14.2%), intra-individual variants (NUMTs, heteroplasmy; 11.3%) and cross-sample contamination (7.5%). Authentication success and the proportions of failure categories varied markedly across trap types, sampling campaigns, taxonomic groups and sequencing runs. We identified 930 confirmed NUMTs based on consistent co-occurrence patterns and phylogenetic proximity to authenticated haplotypes. Single-specimen HTS data contain substantial biological and technical complexity not resolved by standard filtering methods. Our pipeline-agnostic, phylogenetically informed authentication framework achieves robust recovery of validated barcodes while retaining informative secondary variants, improving the accuracy of molecular ASV data to a standard sufficient for inclusion in barcode reference databases and the phylogenetically informed DNA barcoding of tropical insects.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70178","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148409780","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":"Single-Cell Transcriptomics and Development of Gametocyte-Specific Molecular Markers for Avian Malaria Parasites","authors":"A. Berthomieu,&nbsp;I. Rizos,&nbsp;J. W. Bagnoli,&nbsp;S. Gandon,&nbsp;A. M. Talman,&nbsp;A. Rivero","doi":"10.1111/1755-0998.70157","DOIUrl":"10.1111/1755-0998.70157","url":null,"abstract":"<p>Avian malaria, caused by <i>Plasmodium</i> parasites, poses a significant threat to bird populations worldwide, particularly in vulnerable island ecosystems. Yet, progress in understanding avian malaria transmission dynamics has been hampered by the lack of molecular tools to quantify and sex the transmissible stages of the parasite: the male and female gametocytes. This challenge is compounded by the nucleated erythrocytes of avian hosts and the absence of an in vitro culture system, which have historically hindered the advancement of molecular approaches. Here, we develop and validate the first molecular markers to discriminate between asexual, male and female gametocytes in the widespread avian malaria parasite <i>Plasmodium relictum</i>. Using single-cell RNA sequencing and orthology-guided stage mapping, we identified conserved, stage-specific transcripts and leveraged this information to develop molecular markers capable of quantifying and distinguishing male and female gametocytes in two parasite cyt-b lineages, pSGS1 and pDELURB4. These markers outperformed microscopy in sensitivity, detected gametocytes earlier and for longer and revealed consistently higher male-to-female gametocyte ratios than estimated by blood smears. The high degree of conservation of these markers across <i>Plasmodium</i> species suggests broad applicability of these markers to other avian lineages.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70157","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148395477","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":"EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes","authors":"Yunyun Lv,&nbsp;Yanping Li,&nbsp;Jia Li,&nbsp;Xidong Mu","doi":"10.1111/1755-0998.70176","DOIUrl":"10.1111/1755-0998.70176","url":null,"abstract":"<p>Accurate identification of centromeres in telomere-to-telomere (T2T) genomes remains difficult due to the rapid evolution of centromeric repeats and their lack of conserved sequence features. In this study, we present EasyCen, a lightweight sequence-based framework for centromere identification and repeat-architecture profiling across various eukaryotes. Rather than relying on repeat annotation or homology, EasyCen recognises centromeres based on recurrent positional features of repetitive DNA. Besides centromere localisation, EasyCen incorporates a repeat-pair profiling module for exploratory characterisation of internal repeat organisation. Benchmarking on <i>Arabidopsis thaliana</i> and <i>Mus musculus</i> showed high accuracy (typically &gt; 85% coordinate overlap with published annotations) and substantially reduced runtime. Cross-species analysis revealed a ‘beads-on-a-string’-like repeat pattern in both mouse and human centromeres, associated with GC- and CpG-rich subdomains. EasyCen performs effectively without pre-existing repeat libraries, making it particularly useful for large, repeat-rich, or non-model genomes. Our analyses further suggest that certain organisational features of centromeric repeats may recur across diverse eukaryotic lineages despite rapid sequence turnover.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 5","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70176","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148366198","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}