{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T09:11:22Z","timestamp":1789031482811,"version":"build-2803163510"},"reference-count":65,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D program of China","doi-asserted-by":"publisher","award":["2021YFD1600400"],"award-info":[{"award-number":["2021YFD1600400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shaanxi Academy of Sciences Platform Project","award":["2025k-37"],"award-info":[{"award-number":["2025k-37"]}]},{"award":["2025k-37"],"award-info":[{"award-number":["2025k-37"]}],"id":[{"id":"https:\/\/ror.org\/02s9v8n82","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Fungi","JoF"],"abstract":"<jats:p>Coprinellus comprises mushroom-forming saprotrophic fungi that colonize decomposing plant-derived substrates, yet chromosome-complete genomic resources for this genus remain limited. To resolve chromosome architecture and lineage-specific evolution in this fungal group, we generated chromosome-complete assemblies of Coprinellus xanthothrix and C. saccharinus by integrating Oxford Nanopore Technologies (ONT) long reads, DNA nanoball sequencing (DNBSEQ) short reads, Hi-C, and RNA-seq data. Each genome comprised 13 gapless chromosomes with all 26 telomeres recovered; assembly sizes were 46.92 and 54.81 Mb, with BUSCO completeness of 99.20% and 99.10%, respectively. The larger C. saccharinus genome was primarily associated with greater retroelement content, whereas functional annotation profiles and CAZyme repertoires were broadly comparable between species. Phylogenomic analyses grouped C. xanthothrix with C. radians and C. saccharinus with C. micaceus, with estimated divergence times of 54.4 and 32.8 Ma, respectively. Both divergence events occurred within the Paleogene. Gene family analyses identified lineage-specific expansions enriched in nucleotide metabolism, DNA replication and repair, glutathione metabolism, redox regulation, endocytosis, cytoskeletal organization, and cell-cycle processes. Synteny and Ks analyses further revealed chromosome-level rearrangements and lineage-specific small-scale duplication but no strong evidence of recent whole-genome duplication. Together, the temporal placement of these divergences and the associated genomic patterns raise a testable hypothesis that long-term climatic and vegetation reorganization, together with changes in plant-derived substrates and microhabitats, may have contributed to lineage establishment and ecological differentiation. However, because direct paleoecological evidence and functional validation are currently lacking, this proposed relationship should not be interpreted as causal. These chromosome-complete assemblies provide important resources for comparative genomics in Coprinellus and future experimental studies of saprotrophic adaptation.<\/jats:p>","DOI":"10.3390\/jof12090678","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T08:07:41Z","timestamp":1789027661000},"page":"678","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Telomere-to-Telomere Genome Assemblies of Coprinellus xanthothrix and Coprinellus saccharinus Reveal Chromosome-Scale Genome Architecture and Lineage-Specific Evolutionary Dynamics"],"prefix":"10.3390","volume":"12","author":[{"given":"Minghan","family":"Yang","sequence":"first","affiliation":[{"name":"School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China"},{"name":"Fungal Research Center, Shaanxi Provincial Institute of Microbiology, Xi\u2019an 710043, 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Rev. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"5394","DOI":"10.1038\/s41467-022-32924-7","article-title":"Telomere-to-telomere genome sequence of the model mould pathogen Aspergillus fumigatus","volume":"13","author":"Bowyer","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"14653","DOI":"10.1038\/s41598-020-71043-5","article-title":"Telomere-to-telomere assembled and centromere annotated genomes of the two main subspecies of the button mushroom Agaricus bisporus reveal especially polymorphic chromosome ends","volume":"10","author":"Sonnenberg","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Wang, M., Meng, G., Yang, Y., Wang, X., Xie, R., and Dong, C. (2024). Telomere-to-telomere genome assembly of Tibetan medicinal mushroom Ganoderma leucocontextum and the first Copia centromeric retrotransposon in macro-fungi genome. J. Fungi, 10.","DOI":"10.3390\/jof10010015"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1038\/s41597-025-05260-w","article-title":"Haplotype-resolved telomere-to-telomere genome assembly of the dikaryotic fungus pathogen Rhizoctonia cereal","volume":"12","author":"Han","year":"2025","journal-title":"Sci. Data"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"203","DOI":"10.2307\/1224525","article-title":"Coprinus Pers. and the disposition of Coprinus species sensu lato","volume":"50","author":"Redhead","year":"2001","journal-title":"Taxon"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"254","DOI":"10.3852\/11-149","article-title":"Phylogeny and species delimitation in the genus Coprinellus with special emphasis on the haired species","volume":"104","author":"Nagy","year":"2012","journal-title":"Mycologia"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"11889","DOI":"10.1073\/pnas.1003391107","article-title":"Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)","volume":"107","author":"Stajich","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e0250024","DOI":"10.48130\/sif-0025-0024","article-title":"Status review of the distribution, biological compounds, and bioactivities of Coprinellus mushrooms, and their medicinal and biotechnological prospects","volume":"10","author":"Fabros","year":"2025","journal-title":"Stud. Fungi"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-016-1103-0","article-title":"The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community","volume":"17","author":"Jain","year":"2016","journal-title":"Genome Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.1181498","article-title":"Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays","volume":"327","author":"Drmanac","year":"2010","journal-title":"Science"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Williams","year":"2009","journal-title":"Science"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: A revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"Marcais","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes","volume":"11","author":"Jaron","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_18","unstructured":"Krueger, F. (2026, July 20). Trim Galore: A Wrapper Tool Around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ Files. Babraham Bioinformatics. Available online: https:\/\/github.com\/FelixKrueger\/TrimGalore."},{"key":"ref_19","unstructured":"Wick, R.R. (2026, July 20). Filtlong: A Tool for Filtering Long Reads by Quality. GitHub. Available online: https:\/\/github.com\/rrwick\/Filtlong."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41467-020-20236-7","article-title":"Efficient assembly of nanopore reads via highly accurate and intact error correction","volume":"12","author":"Chen","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1101\/gr.214270.116","article-title":"Fast and accurate de novo genome assembly from long uncorrected reads","volume":"27","author":"Vaser","year":"2017","journal-title":"Genome Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Vasimuddin, M., Misra, S., Li, H., and Aluru, S. (2019). Efficient architecture-aware acceleration of BWA-MEM for multicore systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), IEEE.","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., and Young, S.K. (2014). Pilon: An integrated tool for comprehensive microbial variant detection and assembly improvement. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112963"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Dudchenko, O., Shamim, M.S., Batra, S.S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., St Hilaire, B.G., Yao, W., and Stamenova, E. (2018). The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv, 254797.","DOI":"10.1101\/254797"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies","volume":"21","author":"Rhie","year":"2020","journal-title":"Genome Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Simao","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"W177","DOI":"10.1093\/nar\/gkaa220","article-title":"Galaxy HiCExplorer 3: A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization","volume":"48","author":"Wolff","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","first-page":"4.10.1","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"25","author":"Chen","year":"2009","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase Update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mob. DNA"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1093\/bioinformatics\/btv661","article-title":"BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS","volume":"32","author":"Hoff","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1101\/gr.6743907","article-title":"MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes","volume":"18","author":"Cantarel","year":"2008","journal-title":"Genome Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"giz100","DOI":"10.1093\/gigascience\/giz100","article-title":"rnaSPAdes: A de novo transcriptome assembler and its application to RNA-Seq data","volume":"8","author":"Bushmanova","year":"2019","journal-title":"GigaScience"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"W309","DOI":"10.1093\/nar\/gkh379","article-title":"AUGUSTUS: A web server for gene finding in eukaryotes","volume":"32","author":"Stanke","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"W95","DOI":"10.1093\/nar\/gky418","article-title":"dbCAN2: A meta server for automated carbohydrate-active enzyme annotation","volume":"46","author":"Zhang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Eddy, S.R. (2011). Accelerated profile HMM searches. PLoS Comput. Biol., 7.","DOI":"10.1371\/journal.pcbi.1002195"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Busk, P.K., Pilgaard, B., Lezyk, M.J., Meyer, A.S., and Lange, L. (2017). Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function. BMC Bioinform., 18.","DOI":"10.1186\/s12859-017-1625-9"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: An information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: Phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Zhang, C., Rabiee, M., Sayyari, E., and Mirarab, S. (2018). ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform., 19.","DOI":"10.1186\/s12859-018-2129-y"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: Phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"msac174","DOI":"10.1093\/molbev\/msac174","article-title":"TimeTree 5: An expanded resource for species divergence times","volume":"39","author":"Kumar","year":"2022","journal-title":"Mol. Biol. Evol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1093\/bioinformatics\/btl097","article-title":"CAFE: A computational tool for the study of gene family evolution","volume":"22","author":"Cristianini","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_55","first-page":"100141","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"e211","DOI":"10.1002\/imt2.211","article-title":"JCVI: A versatile toolkit for comparative genomics analysis","volume":"3","author":"Tang","year":"2024","journal-title":"iMeta"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1093\/bioinformatics\/bty915","article-title":"wgd: Simple command line tools for the analysis of ancient whole-genome duplications","volume":"35","author":"Zwaenepoel","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"e01287-15","DOI":"10.1128\/genomeA.01287-15","article-title":"Draft genome sequence of the fungus Trametes hirsuta 072","volume":"3","author":"Pavlov","year":"2015","journal-title":"Genome Announc."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Moiseenko, K.V., Glazunova, O.A., Shakhova, N.V., Savinova, O.S., Vasina, D.V., Tyazhelova, T.V., Psurtseva, N.V., and Fedorova, T.V. (2019). Fungal adaptation to the advanced stages of wood decomposition: Insights from the Steccherinum ochraceum. Microorganisms, 7.","DOI":"10.3390\/microorganisms7110527"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Levasseur, A., Lomascolo, A., Chabrol, O., Ruiz-Due\u00f1as, F.J., Boukhris-Uzan, E., Piumi, F., K\u00fces, U., Ram, A.F.J., Murat, C., and Haon, M. (2014). The genome of the white-rot fungus Pycnoporus cinnabarinus: A basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-486"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1080\/12298093.2020.1725361","article-title":"Comparative genomics uncovers the genetic diversity and synthetic biology of secondary metabolite production of Trametes","volume":"48","author":"Zhang","year":"2020","journal-title":"Mycobiology"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nature06588","article-title":"An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics","volume":"451","author":"Zachos","year":"2008","journal-title":"Nature"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1383","DOI":"10.1126\/science.aba6853","article-title":"An astronomically dated record of Earth\u2019s climate and its predictability over the last 66 million years","volume":"369","author":"Westerhold","year":"2020","journal-title":"Science"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1146\/annurev-earth-040610-133431","article-title":"The Paleocene-Eocene Thermal Maximum: A perturbation of carbon cycle, climate, and biosphere with implications for the future","volume":"39","author":"McInerney","year":"2011","journal-title":"Annu. Rev. Earth Planet. Sci."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1126\/science.1193833","article-title":"Effects of rapid global warming at the Paleocene-Eocene boundary on Neotropical vegetation","volume":"330","author":"Jaramillo","year":"2010","journal-title":"Science"}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/9\/678\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T08:54:38Z","timestamp":1789030478000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/9\/678"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,10]]},"references-count":65,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["jof12090678"],"URL":"https:\/\/doi.org\/10.3390\/jof12090678","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,10]]}}}