{"doi":"10.1093/gigascience/giaf009","title":"The telomere-to-telomere genome of flowering cherry (<i>Prunus campanulata</i>) reveals genomic evolution of the subgenus <i>Cerasus</i>","abstract":"<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Prunus campanulata, a species of ornamental cherry, holds significant genetic and horticultural value. Despite the availability of various cherry genomes, a fully resolved telomere-to-telomere (T2T) assembly for this species has been lacking. Recent advancements in long-read sequencing technologies have made it possible to generate gap-free genome assemblies, providing comprehensive insights into genomic structures that were previously inaccessible.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Findings</jats:title>\n                  <jats:p>We present the first T2T genome assembly for P. campanulata “Lianmeiren” (v2.0), achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, Illumina, and Hi-C sequencing. The assembly resulted in a highly contiguous genome with a total size of 266.23 Mb and a contig N50 of 31.6 Mb. The genome exhibits remarkable completeness (98.9% BUSCO) and high accuracy (quality value of 48.75). Additionally, 13 telomeres and putative centromere regions were successfully identified across the 8 pseudochromosomes. Comparative analysis with the previous v1.0 assembly revealed 336,943 single nucleotide polymorphisms, 107,521 indels, and 1,413 structural variations, along with the annotation of 1,402 new genes.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>This T2T genome assembly of P. campanulata “Lianmeiren” provides a critical reference for understanding the genetic architecture of the species. It enhances our ability to study structural variations, gene function, and evolutionary biology within the Prunus genus.</jats:p>\n               </jats:sec>","journal":"GigaScience","year":2025,"id":640663,"datarank":0.26876392038420827,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.0,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1665156,"name":"Yingang Li","orcid":"0000-0002-3680-281X","position":1,"is_corresponding":false},{"id":1665157,"name":"Fei Zhuge","orcid":null,"position":2,"is_corresponding":false},{"id":81080,"name":"Qi Zhou","orcid":"0000-0002-5084-8697","position":3,"is_corresponding":false},{"id":1665158,"name":"Wenjin Zong","orcid":null,"position":4,"is_corresponding":false},{"id":1665159,"name":"Xinhong Liu","orcid":null,"position":5,"is_corresponding":false},{"id":658060,"name":"Xin Shen","orcid":"0000-0003-4429-8358","position":6,"is_corresponding":false},{"id":1665154,"name":"Dongyue Jiang","orcid":"0000-0001-7467-5738","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The telomere-to-telomere genome of flowering cherry (<i>Prunus campanulata</i>) reveals genomic evolution of the subgenus <i>Cerasus</i>","abstract":"<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Prunus campanulata, a species of ornamental cherry, holds significant genetic and horticultural value. Despite the availability of various cherry genomes, a fully resolved telomere-to-telomere (T2T) assembly for this species has been lacking. Recent advancements in long-read sequencing technologies have made it possible to generate gap-free genome assemblies, providing comprehensive insights into genomic structures that were previously inaccessible.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Findings</jats:title>\n                  <jats:p>We present the first T2T genome assembly for P. campanulata “Lianmeiren” (v2.0), achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, Illumina, and Hi-C sequencing. The assembly resulted in a highly contiguous genome with a total size of 266.23 Mb and a contig N50 of 31.6 Mb. The genome exhibits remarkable completeness (98.9% BUSCO) and high accuracy (quality value of 48.75). Additionally, 13 telomeres and putative centromere regions were successfully identified across the 8 pseudochromosomes. Comparative analysis with the previous v1.0 assembly revealed 336,943 single nucleotide polymorphisms, 107,521 indels, and 1,413 structural variations, along with the annotation of 1,402 new genes.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>This T2T genome assembly of P. campanulata “Lianmeiren” provides a critical reference for understanding the genetic architecture of the species. It enhances our ability to study structural variations, gene function, and evolutionary biology within the Prunus genus.</jats:p>\n               </jats:sec>","is_dataset_classified":null,"base_score":1.791759469228055,"endowment":1.791759469228055,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39982852","pmcid":"PMC11843098","openalex_id":"https://openalex.org/W4407862080","authors":[],"funders":[{"funder_name":"Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding","grant_id":"2021C02071-4","title":null},{"funder_name":"Special Support Funds of Zhejiang for Scientific Research Institutes","grant_id":"2023F1068-2","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"32101585","title":null}],"total_grants":3,"fwci":4.5056,"citation_percentile":0.93430192,"influential_citations":0,"citation_trend":[{"year":2025,"count":2},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1093/gigascience/giaf009","host_type":"journal"},{"url":"https://doi.org/10.1093/gigascience/giaf009","host_type":"publisher"},{"url":"https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giaf009/62043132/giaf009.pdf","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39982852","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11843098","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11843098","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11843098?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Chromosomal and Genetic Variations","Telomeres, Telomerase, and Senescence","Genomics and Phylogenetic Studies","Telomere","Genome, Plant","Evolution, Molecular","Prunus","Genomics","Molecular Sequence Annotation","Phylogeny"],"mesh_terms":["Phylogeny","Telomere","Genome, Plant","Evolution, Molecular","Genomics","Prunus","Molecular Sequence Annotation","High-Throughput Nucleotide Sequencing"],"keywords":["Genome","Sequence assembly","Biology","Contig","Indel","Genome size","Prunus","Reference genome","Genetics","Telomere","Nanopore sequencing","Centromere","Subgenus","Computational biology","Gene","Single-nucleotide polymorphism","Botany","Genus","Chromosome","Genotype","Comparative genomics","Structural Variations","Prunus Campanulata","Cherry Genomics","T2t Genome"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"rrid"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-07T13:10:52.100527Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}