{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T13:01:49Z","timestamp":1791378109799,"version":"4.3.2"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"10","funder":[{"DOI":"10.13039\/100014455","name":"University of Tennessee","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014455","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"USDA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100022918","name":"ARS","doi-asserted-by":"publisher","award":["NACA 58-6062-6"],"award-info":[{"award-number":["NACA 58-6062-6"]}],"id":[{"id":"10.13039\/501100022918","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100022918","name":"ARS","doi-asserted-by":"publisher","award":["6066-21310-006-00D"],"award-info":[{"award-number":["6066-21310-006-00D"]}],"id":[{"id":"10.13039\/501100022918","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Kousa dogwood (Cornus kousa Hance) is a popular flowering ornamental tree in the United States, largely due to its pest and disease tolerance. Here, we present the first chromosome-scale, diploid genome assembly of C. kousa K2, a foundational breeding parent. The final chromosome-scale genome assemblies are 1602.739 Mb for Hap 1 and 1598.929 Mb for Hap 2. The complete Benchmarking Universal Single-Copy Orthologs (BUSCO) for Hap 1 and 2 were 98.8 and 98.4%, respectively. Between the 2 haplotypes, 98.97% of the genome is placed into chromosomes. 30,799 and 31,044 genes were annotated in Hap 1 and Hap 2, respectively. This annotated genome assembly for C. kousa provides insight into the genomic composition of the species and will enhance our understanding of the genetic control of traits of interest in breeding programs and the evolutionary history of the Cornus genus.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag229","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:54:27Z","timestamp":1787165667000},"source":"Crossref","is-referenced-by-count":0,"title":["First chromosome-scale genome of\n                    <i>Cornus kousa<\/i>\n                    K2"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7572-0967","authenticated-orcid":false,"given":"Trinity P H","family":"Mehler","sequence":"first","affiliation":[{"name":"Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN 37996 ,","place":["United States"]},{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah L","family":"Boggess","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN 37996 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2655-5464","authenticated-orcid":false,"given":"Marcin","family":"Nowicki","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN 37996 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denita","family":"Hadziabdic","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN 37996 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"DeWayne","family":"Shoemaker","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN 37996 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert N","family":"Trigiano","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN 37996 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William E","family":"Klingeman","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences, University of Tennessee , Knoxville, TN 37996-4500 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas J","family":"Molnar","sequence":"additional","affiliation":[{"name":"Department of Plant Biology, Rutgers University , New Brunswick, NJ 08901 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheron A","family":"Simpson","sequence":"additional","affiliation":[{"name":"Genomics and Bioinformatics Research Unit, United States Department of Agriculture\u2014Agriculture Research Service (USDA-ARS) , Stoneville, MS 38776 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9728-5214","authenticated-orcid":false,"given":"Ramey C","family":"Youngblood","sequence":"additional","affiliation":[{"name":"Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University , Starkville, MS 39759 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9670-9433","authenticated-orcid":false,"given":"Amanda M","family":"Hulse-Kemp","sequence":"additional","affiliation":[{"name":"Genomics and Bioinformatics Research Unit, USDA-ARS , Raleigh, NC 27695 ,","place":["United States"]},{"name":"Department of Crop and Soil Sciences, North Carolina State University , Raleigh, NC 27695 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian E","family":"Scheffler","sequence":"additional","affiliation":[{"name":"Genomics and Bioinformatics Research Unit, United States Department of Agriculture\u2014Agriculture Research Service (USDA-ARS) , Stoneville, MS 38776 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2971-9353","authenticated-orcid":false,"given":"Margaret E","family":"Staton","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN 37996 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,19]]},"reference":[{"key":"2026100708173430600_jkag229-B1","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s13059-024-03198-7","article-title":"Rapid and sensitive detection of genome contamination at scale with FCS-GX","volume":"25","author":"Astashyn","year":"2024","journal-title":"Genome Biol"},{"key":"2026100708173430600_jkag229-B2","author":"Bushnell","year":"2022"},{"key":"2026100708173430600_jkag229-B3","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/j.gpb.2019.04.002","article-title":"gFACs: gene filtering, analysis, and conversion to unify genome annotations across alignment and gene prediction frameworks","volume":"17","author":"Caballero","year":"2019","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2026100708173430600_jkag229-B4","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2026100708173430600_jkag229-B5","volume-title":"Dogwoods: the genus Cornus","author":"Cappiello","year":"2005"},{"key":"2026100708173430600_jkag229-B6","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"Cheng","year":"2021","journal-title":"Nat Methods"},{"key":"2026100708173430600_jkag229-B7","doi-asserted-by":"publisher","first-page":"159","DOI":"10.48044\/jauf.1988.040","article-title":"Cause and control of dogwood anthracnose in northeastern United States","volume":"14","author":"Daughtrey","year":"1988","journal-title":"Arboric Urban For"},{"key":"2026100708173430600_jkag229-B8","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2026100708173430600_jkag229-B9","doi-asserted-by":"publisher","DOI":"10.1093\/dnares\/dsac051","article-title":"Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae","volume":"30","author":"Dong","year":"2023","journal-title":"DNA Res"},{"key":"2026100708173430600_jkag229-B10","doi-asserted-by":"publisher","DOI":"10.1002\/ajb2.16116","article-title":"An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data","volume":"110","author":"Du","year":"2023","journal-title":"Am J Bot"},{"key":"2026100708173430600_jkag229-B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/jse.13037","article-title":"RAD-seq data provide new insights into biogeography, diversity anomaly, and species delimitation in eastern Asian\u2013north American disjunct clade Benthamidia of Cornus (Cornaceae)","volume":"62","author":"Du","year":"2024","journal-title":"J Syst Evol"},{"key":"2026100708173430600_jkag229-B12","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"key":"2026100708173430600_jkag229-B13","doi-asserted-by":"publisher","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":"2026100708173430600_jkag229-B14","doi-asserted-by":"publisher","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 U S A"},{"key":"2026100708173430600_jkag229-B15","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2019.106601","article-title":"Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous","volume":"140","author":"Fu","year":"2019","journal-title":"Mol Phylogenet Evol"},{"key":"2026100708173430600_jkag229-B16","doi-asserted-by":"publisher","first-page":"2922","DOI":"10.1093\/bioinformatics\/btac196","article-title":"Plotsr: visualizing structural similarities and rearrangements between multiple genomes","volume":"38","author":"Goel","year":"2022","journal-title":"Bioinformatics"},{"key":"2026100708173430600_jkag229-B17","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1186\/s13059-019-1911-0","article-title":"SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies","volume":"20","author":"Goel","year":"2019","journal-title":"Genome Biol"},{"key":"2026100708173430600_jkag229-B18","doi-asserted-by":"publisher","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026100708173430600_jkag229-B19","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/s12870-025-07836-5","article-title":"Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts","volume":"26","author":"Hamm","year":"2025","journal-title":"BMC Plant Biol"},{"key":"2026100708173430600_jkag229-B20","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2025.1735902","article-title":"Ornamental origins and genomic frontiers: a review of big-bracted dogwood research","volume":"16","author":"Hamm","year":"2026","journal-title":"Front Plant Sci"},{"key":"2026100708173430600_jkag229-B21","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.251","article-title":"RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms","volume":"6","author":"Hao","year":"2020","journal-title":"PeerJ Comput Sci"},{"key":"2026100708173430600_jkag229-B22","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1111\/1755-0998.13106","article-title":"EnTAP: bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes","volume":"20","author":"Hart","year":"2020","journal-title":"Mol Ecol Resour"},{"key":"2026100708173430600_jkag229-B23","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhad196","article-title":"A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development","volume":"10","author":"He","year":"2023","journal-title":"Hortic Res"},{"key":"2026100708173430600_jkag229-B24","doi-asserted-by":"publisher","first-page":"5573","DOI":"10.1038\/s41467-024-49912-8","article-title":"HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation","volume":"15","author":"Hu","year":"2024","journal-title":"Nat Commun"},{"key":"2026100708173430600_jkag229-B25","doi-asserted-by":"publisher","first-page":"D81","DOI":"10.1093\/nar\/gkv1272","article-title":"The Dfam database of repetitive DNA families","volume":"44","author":"Hubley","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026100708173430600_jkag229-B26","doi-asserted-by":"publisher","first-page":"D445","DOI":"10.1093\/nar\/gkac998","article-title":"OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity","volume":"51","author":"Kuznetsov","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026100708173430600_jkag229-B27","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"2026100708173430600_jkag229-B28","doi-asserted-by":"publisher","DOI":"10.3390\/genes8100290","article-title":"Chromosome evolution in connection with repetitive sequences and epigenetics in plants","volume":"8","author":"Li","year":"2017","journal-title":"Genes (Basel)"},{"key":"2026100708173430600_jkag229-B29","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1094\/PDIS-93-11-1084","article-title":"Powdery mildew of dogwoods: current status and future prospects","volume":"93","author":"Li","year":"2009","journal-title":"Plant Dis"},{"key":"2026100708173430600_jkag229-B30","doi-asserted-by":"publisher","DOI":"10.1093\/plphys\/kiaf077","article-title":"The parsley genome assembly and DNA methylome shed light on apigenin biosynthesis in the Apiaceae","volume":"197","author":"Liu","year":"2025","journal-title":"Plant Physiol"},{"key":"2026100708173430600_jkag229-B31","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO Update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral Genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026100708173430600_jkag229-B32","doi-asserted-by":"publisher","first-page":"93","DOI":"10.3897\/phytokeys.55.9112","article-title":"Cornus \u00d7 elwinortonii and Cornus \u00d7 rutgersensis (Cornaceae), new names for two artificially produced hybrids of big-bracted dogwoods","volume":"55","author":"Mattera","year":"2015","journal-title":"PhytoKeys"},{"key":"2026100708173430600_jkag229-B33","doi-asserted-by":"publisher","DOI":"10.3390\/biology11040488","article-title":"Specificities and dynamics of transposable elements in land plants","volume":"11","author":"Mhiri","year":"2022","journal-title":"Biology (Basel)"},{"key":"2026100708173430600_jkag229-B34","doi-asserted-by":"publisher","first-page":"271","DOI":"10.17660\/ActaHortic.2013.990.32","article-title":"The Rutgers university woody ornamentals breeding program: past, present, and future","volume":"990","author":"Molnar","year":"2013","journal-title":"Acta Hortic"},{"key":"2026100708173430600_jkag229-B35","doi-asserted-by":"publisher","first-page":"e0307326","DOI":"10.1371\/journal.pone.0307326","article-title":"Genetic diversity analysis of big-bracted dogwood (Cornus florida and C. kousa) cultivars, interspecific hybrids, and wild-collected accessions using RADseq","volume":"19","author":"Moreau","year":"2024","journal-title":"PLoS One"},{"key":"2026100708173430600_jkag229-B36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1012164","article-title":"Pairtools: from sequencing data to chromosome contacts","volume":"20","author":"Open2C","year":"2024","journal-title":"PLOS Comput Biol"},{"key":"2026100708173430600_jkag229-B37","doi-asserted-by":"publisher","DOI":"10.3390\/horticulturae8050405","article-title":"High-density linkage mapping and identification of quantitative trait loci associated with powdery mildew resistance in flowering dogwood (Cornus florida)","volume":"8","author":"Pfarr Moreau","year":"2022","journal-title":"Horticulturae"},{"key":"2026100708173430600_jkag229-B38","doi-asserted-by":"publisher","first-page":"1736","DOI":"10.1038\/s41597-025-06024-2","article-title":"A high-quality chromosome-level genome assembly of herbaceous bamboo species Lithachne pauciflora","volume":"12","author":"Qian","year":"2025","journal-title":"Sci Data"},{"key":"2026100708173430600_jkag229-B39","doi-asserted-by":"publisher","first-page":"11","DOI":"10.48044\/jauf.1995.003","article-title":"Susceptibility of cultivars and hybrids of kousa dogwood to dogwood anthracnose and powdery mildew","volume":"21","author":"Ranney","year":"1995","journal-title":"Arboric Urban For"},{"key":"2026100708173430600_jkag229-B40","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2026"},{"key":"2026100708173430600_jkag229-B41","doi-asserted-by":"publisher","first-page":"825","DOI":"10.21273\/HORTSCI.48.7.825","article-title":"Ploidy levels and relative genome sizes of species, hybrids, and cultivars of dogwood (Cornus spp.)","volume":"48","author":"Shearer","year":"2013","journal-title":"HortScience"},{"key":"2026100708173430600_jkag229-B42","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhad061","article-title":"The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding","volume":"10","author":"Shi","year":"2023","journal-title":"Hortic Res"},{"key":"2026100708173430600_jkag229-B43","author":"Smit","year":"2013"},{"key":"2026100708173430600_jkag229-B44","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1016\/j.gpb.2022.11.002","article-title":"A chromosome-level reference genome of African oil palm provides insights into its divergence and stress adaptation","volume":"21","author":"Wang","year":"2023","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2026100708173430600_jkag229-B45","doi-asserted-by":"publisher","first-page":"6133","DOI":"10.1073\/pnas.1700073114","article-title":"Wild tobacco genomes reveal the evolution of nicotine biosynthesis","volume":"114","author":"Xu","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026100708173430600_jkag229-B46","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1186\/s13059-025-03676-6","article-title":"Oatk: a de novo assembly tool for complex plant organelle genomes","volume":"26","author":"Zhou","year":"2025","journal-title":"Genome Biol"},{"key":"2026100708173430600_jkag229-B47","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac808","article-title":"YaHS: yet another Hi-C scaffolding tool","volume":"39","author":"Zhou","year":"2023","journal-title":"Bioinformatics"}],"container-title":["G3: Genes, Genomes, Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/g3journal\/advance-article-pdf\/doi\/10.1093\/g3journal\/jkag229\/70715526\/jkag229.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/16\/10\/jkag229\/70715526\/jkag229.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/16\/10\/jkag229\/70715526\/jkag229.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T12:18:04Z","timestamp":1791375484000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/g3journal\/article\/doi\/10.1093\/g3journal\/jkag229\/8766636"}},"subtitle":[],"editor":[{"given":"T","family":"Pyh\u00e4j\u00e4rvi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,19]]},"references-count":47,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,8,19]]},"published-print":{"date-parts":[[2026,10,7]]}},"URL":"https:\/\/doi.org\/10.1093\/g3journal\/jkag229","relation":{},"ISSN":["2160-1836"],"issn-type":[{"value":"2160-1836","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,8,19]]},"article-number":"jkag229"}}