{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:53:37Z","timestamp":1790902417665,"version":"4.1.0"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T00:00:00Z","timestamp":1779235200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Engineering Research & Innovation Team Project of Beijing Forestry University","award":["BLRC2023C01"],"award-info":[{"award-number":["BLRC2023C01"]}],"id":[{"id":"https:\/\/ror.org\/04xv2pc41","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Science and Technology Innovation Programs of Beijing Forestry University","award":["2025ZLXD02"],"award-info":[{"award-number":["2025ZLXD02"]}],"id":[{"id":"https:\/\/ror.org\/04xv2pc41","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32271831"],"award-info":[{"award-number":["32271831"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the National Key R&D Program of China","award":["2022YFD2200603 and 2023YFD2201801"],"award-info":[{"award-number":["2022YFD2200603 and 2023YFD2201801"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Understanding how plants adapt to extreme cold and ripen fruit is a key question in plant biology. Lonicera caerulea (blue honeysuckle), a cold-tolerant berry species native to the northern temperate zone, is valued as a \u2018noble fruit\u2019 for its rich nutrient profile and serves as an ideal model for studies due to its unique ability to thrive in low temperatures and ripen fruit during early spring. Here, we generated a chromosome-level genome assembly for wild L. caerulea from the Changbai Mountain region. We integrated it with transcriptomic and metabolomic analyses to explore its molecular cold adaptation mechanisms. We found that L. caerulea achieves cold tolerance and fruit ripening through dynamic regulation of two important metabolic pathways. Under cold stress, the LcODO1\/LcMYB15\u2013LcSLAS module promotes iridoid accumulation, while the LcbHLH62\/LcMYB3R5\u2013LcF3GT module enhances anthocyanin biosynthesis, jointly increasing plant cold resistance. During fruit maturation, metabolite profiles show dynamic reprogramming: anthocyanin levels rise in both pulp and peel, while the content of bitter iridoids markedly decreases in the pulp. This work provides a comprehensive genomic framework for understanding cold adaptation mechanisms, offering valuable gene resources and a theoretical foundation for improving cold resistance and fruit quality in breeding programs.<\/jats:p>","DOI":"10.1093\/hr\/uhag198","type":"journal-article","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T00:44:36Z","timestamp":1779324276000},"source":"Crossref","is-referenced-by-count":0,"title":["Adaptive cold-environmental strategies of\n                    <i>Lonicera caerulea<\/i>\n                    : synergistic regulation of anthocyanin and iridoid pathways in cold tolerance and fruit ripening"],"prefix":"10.1093","volume":"13","author":[{"given":"Tianyi","family":"Wang","sequence":"first","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]},{"name":"Beijing Key Laboratory of Efficient Biosynthesis of Plant Secondary Metabolites , Beijing Forestry University, Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-0220","authenticated-orcid":false,"given":"Qing","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]},{"name":"Beijing Key Laboratory of Efficient Biosynthesis of Plant Secondary Metabolites , Beijing Forestry University, Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0799-5546","authenticated-orcid":false,"given":"Hongyan","family":"Cao","sequence":"additional","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]},{"name":"Beijing Key Laboratory of Efficient Biosynthesis of Plant Secondary Metabolites , Beijing Forestry University, Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Du","sequence":"additional","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]},{"name":"Beijing Key Laboratory of Efficient Biosynthesis of Plant Secondary Metabolites , Beijing Forestry University, Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baoan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Horticulture, China Agricultural University , Beijing 100193 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuxin","family":"Fan","sequence":"additional","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]},{"name":"Beijing Key Laboratory of Efficient Biosynthesis of Plant Secondary Metabolites , Beijing Forestry University, Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cai","family":"Qin","sequence":"additional","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yadong","family":"Duan","sequence":"additional","affiliation":[{"name":"Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences , Harbin 150081 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0445-0768","authenticated-orcid":false,"given":"Yujie","family":"Fu","sequence":"additional","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]},{"name":"Beijing Key Laboratory of Efficient Biosynthesis of Plant Secondary Metabolites , Beijing Forestry University, Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Meng","sequence":"additional","affiliation":[{"name":"College of Forestry, Beijing Forestry University , Beijing 100000 ,","place":["China"]},{"name":"Beijing Key Laboratory of Efficient Biosynthesis of Plant Secondary Metabolites , Beijing Forestry University, Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,20]]},"reference":[{"key":"2026100119561895000_ref1","doi-asserted-by":"crossref","first-page":"2290","DOI":"10.1093\/jxb\/erac054","article-title":"Elastic and collapsible: current understanding of cell walls in succulent plants","volume":"73","author":"Fradera-Soler","year":"2022","journal-title":"J Exp Bot"},{"key":"2026100119561895000_ref2","doi-asserted-by":"publisher","DOI":"10.1111\/pce.15571","article-title":"Uncovering the secrets of how plants adapt to water stress","author":"Li","year":"2025","journal-title":"Plant Cell Environ"},{"key":"2026100119561895000_ref3","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1007\/s11632-005-0057-1","article-title":"Plant antifreeze proteins and their expression regulatory mechanism","volume":"7","author":"Lin","year":"2005","journal-title":"For Stud China"},{"key":"2026100119561895000_ref4","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/S0031-9422(03)00420-5","article-title":"Antifreeze proteins in higher plants","volume":"64","author":"At\u0131c\u0131","year":"2003","journal-title":"Phytochemistry"},{"key":"2026100119561895000_ref5","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.3389\/fpls.2017.02153","article-title":"Ice-binding proteins in plants","volume":"8","author":"Bredow","year":"2017","journal-title":"Front Plant Sci"},{"key":"2026100119561895000_ref6","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1007\/978-981-99-3334-1_19","volume-title":"Plant Phenolics in Biotic Stress Management","author":"Khanday","year":"2024"},{"key":"2026100119561895000_ref7","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1111\/tpj.15453","article-title":"Volatile terpenes \u2013 mediators of plant-to-plant communication","volume":"108","author":"Rosenkranz","year":"2021","journal-title":"Plant J"},{"key":"2026100119561895000_ref8","article-title":"Advances in the biosynthesis of terpenoids and their ecological functions in plant resistance","volume":"24","author":"Li","year":"2023","journal-title":"Int J Mol Sci"},{"key":"2026100119561895000_ref9","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/978-3-030-27165-7_9","volume-title":"Bioactive Molecules in Plant Defense: Signaling in Growth and Stress","author":"Ali","year":"2019"},{"key":"2026100119561895000_ref10","doi-asserted-by":"crossref","first-page":"9443","DOI":"10.1038\/s41598-020-65932-y","article-title":"Impact of alkaloids in food consumption, metabolism and survival in a blood-sucking insect","volume":"10","author":"Mu\u00f1oz","year":"2020","journal-title":"Sci Rep"},{"key":"2026100119561895000_ref11","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/s10722-018-0701-y","article-title":"Morphological and molecular evaluation of the Far East fruit genetic resources of Lonicera caerulea L.\u2014vegetation, ethnobotany, use and conservation","volume":"66","author":"Holubec","year":"2019","journal-title":"Genet Resour Crop Evol"},{"key":"2026100119561895000_ref12","doi-asserted-by":"crossref","first-page":"8992","DOI":"10.1080\/10408398.2022.2061910","article-title":"Lonicera caerulea (Haskap berries): a review of development traceability, functional value, product development status, future opportunities, and challenges","volume":"63","author":"Cheng","year":"2023","journal-title":"Crit Rev Food Sci Nutr"},{"key":"2026100119561895000_ref13","doi-asserted-by":"crossref","DOI":"10.1016\/j.foodchem.2022.134391","article-title":"Component characteristics and reactive oxygen species scavenging activity of anthocyanins from fruits of Lonicera caerulea L","volume":"403","author":"Fan","year":"2023","journal-title":"Food Chem"},{"key":"2026100119561895000_ref14","doi-asserted-by":"crossref","DOI":"10.1016\/j.foodchem.2024.140150","article-title":"Exploring bitter characteristics of blue honeysuckle (Lonicera caerulea L.) berries by sensory-guided analysis: key bitter compounds and varietal differences","volume":"457","author":"Xia","year":"2024","journal-title":"Food Chem"},{"key":"2026100119561895000_ref15","doi-asserted-by":"crossref","first-page":"6447","DOI":"10.1080\/87559129.2022.2117375","article-title":"A review on bioactive iridoids in edible fruits \u2013 from garden to food and pharmaceutical products","volume":"39","author":"Przybylska","year":"2023","journal-title":"Food Rev Int"},{"key":"2026100119561895000_ref16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/14786419.2025.2477803","article-title":"Lonicera maackii (Rupr.) Maxim: a review of its phytochemistry, pharmacological activities and clinical application","author":"Zhang","year":"2025","journal-title":"Nat Prod Res"},{"key":"2026100119561895000_ref17","doi-asserted-by":"crossref","DOI":"10.1016\/j.plaphy.2023.108090","article-title":"Critical review on anthocyanins in blue honeysuckle (Lonicera caerulea L.) and their function","volume":"204","author":"Guo","year":"2023","journal-title":"Plant Physiol Biochem"},{"key":"2026100119561895000_ref18","doi-asserted-by":"crossref","DOI":"10.1016\/j.foodres.2024.114234","article-title":"Bitter flavors and bitter compounds in foods: identification, perception, and reduction techniques","volume":"183","author":"Chu","year":"2024","journal-title":"Food Res Int"},{"key":"2026100119561895000_ref19","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1146\/annurev-genet-111523-102226","article-title":"Regulatory networks underlying plant responses and adaptation to cold stress","volume":"58","author":"Ding","year":"2024","journal-title":"Annu Rev Genet"},{"key":"2026100119561895000_ref20","doi-asserted-by":"crossref","DOI":"10.1093\/hr\/uhae077","article-title":"Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae)","volume":"11","author":"Zhang","year":"2024","journal-title":"Hortic Res"},{"key":"2026100119561895000_ref21","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.jare.2024.12.038","article-title":"Lonicera caerulea genome reveals molecular mechanisms of freezing tolerance and anthocyanin biosynthesis","volume":"76","author":"Wang","year":"2024","journal-title":"J Adv Res"},{"key":"2026100119561895000_ref22","doi-asserted-by":"crossref","first-page":"2902","DOI":"10.1093\/plphys\/kiad295","article-title":"High-resolution genome mapping and functional dissection of chlorogenic acid production in Lonicera maackii","volume":"192","author":"Li","year":"2023","journal-title":"Plant Physiol"},{"key":"2026100119561895000_ref23","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1093\/molbev\/msy200","article-title":"Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments","volume":"36","author":"Wang","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2026100119561895000_ref24","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1073\/pnas.1423685112","article-title":"Seeing is believing: dynamic evolution of gene families","volume":"112","author":"Harris","year":"2015","journal-title":"Proc Natl Acad Sci"},{"key":"2026100119561895000_ref25","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1016\/j.tplants.2022.01.008","article-title":"Transcriptional regulatory network of plant cold-stress responses","volume":"27","author":"Kidokoro","year":"2022","journal-title":"Trends Plant Sci"},{"key":"2026100119561895000_ref26","doi-asserted-by":"crossref","DOI":"10.1093\/hr\/uhad093","article-title":"Identification of candidate genes that regulate the trade-off between seedling cold tolerance and fruit quality in melon (Cucumis melo L.)","volume":"10","author":"Li","year":"2023","journal-title":"Hortic Res"},{"key":"2026100119561895000_ref27","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1111\/nph.15696","article-title":"Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants","volume":"222","author":"Ding","year":"2019","journal-title":"New Phytol"},{"key":"2026100119561895000_ref28","article-title":"Research progress on the physiological response and molecular mechanism of cold response in plants","volume":"15","author":"Wang","year":"2024","journal-title":"Front Plant Sci"},{"key":"2026100119561895000_ref29","article-title":"Research progress on the biosynthesis, metabolic engineering, and pharmacology of bioactive compounds from the Lonicera genus","volume":"3","author":"Chen","year":"2024","journal-title":"Med Plant Biol"},{"key":"2026100119561895000_ref30","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1016\/j.molp.2018.06.002","article-title":"Phylogenomic mining of the mints reveals multiple mechanisms contributing to the evolution of chemical diversity in Lamiaceae","volume":"11","author":"Boachon","year":"2018","journal-title":"Mol Plant"},{"key":"2026100119561895000_ref31","doi-asserted-by":"crossref","DOI":"10.1093\/hr\/uhac040","article-title":"Hierarchical transcription factor and regulatory network for drought response in Betula platyphylla","volume":"9","author":"Jia","year":"2022","journal-title":"Hortic Res"},{"key":"2026100119561895000_ref32","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1016\/j.phytochem.2011.04.015","article-title":"Coping with toxic plant compounds \u2013 the insect\u2019s perspective on iridoid glycosides and cardenolides","volume":"72","author":"Dobler","year":"2011","journal-title":"Phytochemistry"},{"key":"2026100119561895000_ref33","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.phytochem.2010.09.016","article-title":"Repellent activity of catmint, Nepeta cataria, and iridoid nepetalactone isomers against Afro-tropical mosquitoes, ixodid ticks and red poultry mites","volume":"72","author":"Birkett","year":"2011","journal-title":"Phytochemistry"},{"key":"2026100119561895000_ref34","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.146.3649.1318","article-title":"Catnip: its Raison d'\u00catre","volume":"146","author":"Eisner","year":"1964","journal-title":"Science"},{"key":"2026100119561895000_ref35","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1111\/jipb.13608","article-title":"MdbHLH162 connects the gibberellin and jasmonic acid signals to regulate anthocyanin biosynthesis in apple","volume":"66","author":"An","year":"2024","journal-title":"J Integr Plant Biol"},{"key":"2026100119561895000_ref36","doi-asserted-by":"crossref","first-page":"781","DOI":"10.3390\/molecules23040781","article-title":"Ectopic overexpression of a novel R2R3-MYB, NtMYB2 from Chinese narcissus represses anthocyanin biosynthesis in tobacco","volume":"23","author":"Anwar","year":"2018","journal-title":"Molecules"},{"key":"2026100119561895000_ref37","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/s41477-022-01201-2","article-title":"Root-secreted bitter triterpene modulates the rhizosphere microbiota to improve plant fitness","volume":"8","author":"Zhong","year":"2022","journal-title":"Nat Plants"},{"key":"2026100119561895000_ref38","doi-asserted-by":"crossref","first-page":"1839","DOI":"10.1111\/pbi.70450","article-title":"Reducing the sinapine levels of Camelina sativa seeds through targeted genome editing of REF1","volume":"24","author":"Kelly","year":"2025","journal-title":"Plant Biotechnol J"},{"key":"2026100119561895000_ref39","article-title":"Illustration of the variation in the content of flavanone rutinosides in various citrus germplasms from genetic and enzymatic perspectives","volume":"9","author":"Li","year":"2022","journal-title":"Hortic Res"},{"key":"2026100119561895000_ref40","doi-asserted-by":"crossref","DOI":"10.1111\/tpj.70523","article-title":"Indel mutation in transcription factor PabHLH2 regulates amygdalin accumulation and kernel bitterness in apricot","volume":"124","author":"Zhang","year":"2025","journal-title":"Plant J"},{"key":"2026100119561895000_ref41","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1126\/science.1259215","article-title":"Biosynthesis, regulation, and domestication of bitterness in cucumber","volume":"346","author":"Shang","year":"2014","journal-title":"Science"},{"key":"2026100119561895000_ref42","doi-asserted-by":"crossref","first-page":"689","DOI":"10.3389\/fpls.2018.00689","article-title":"Comparative chloroplast genomics of Dipsacales species: insights into sequence variation, adaptive evolution, and phylogenetic relationships","volume":"9","author":"Fan","year":"2018","journal-title":"Front Plant Sci"},{"key":"2026100119561895000_ref43","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1111\/jse.12745","article-title":"A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily","volume":"59","author":"Wang","year":"2021","journal-title":"J Syst Evol"},{"key":"2026100119561895000_ref44","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.1111\/mec.14092","article-title":"Warm\u2013cold colonization: response of oaks to uplift of the Himalaya\u2013Hengduan Mountains","volume":"26","author":"Meng","year":"2017","journal-title":"Mol Ecol"},{"key":"2026100119561895000_ref45","first-page":"23","article-title":"Phylogeography of Populus koreana reveals an unexpected glacial refugium in Northeast Asia","volume":"3","author":"Wang","year":"2023","journal-title":"For Res"},{"key":"2026100119561895000_ref46","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1080\/17550874.2025.2544674","article-title":"Biogeographic connections between the flora of the Arctic and Qinghai-Tibet Plateau: building on the legacy of Richard Abbott","volume":"18","author":"Cai","year":"2025","journal-title":"Plant Ecol Divers"},{"key":"2026100119561895000_ref47","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":"Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"key":"2026100119561895000_ref48","doi-asserted-by":"crossref","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":"2026100119561895000_ref49","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.12688\/f1000research.7334.1","article-title":"HiCUP: pipeline for mapping and processing Hi-C data","volume":"4","author":"Wingett","year":"2015","journal-title":"F1000Res"},{"key":"2026100119561895000_ref50","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1093\/molbev\/msx319","article-title":"BUSCO applications from quality assessments to gene prediction and phylogenomics","volume":"35","author":"Waterhouse","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2026100119561895000_ref51","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1093\/bioinformatics\/btm071","article-title":"CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes","volume":"23","author":"Parra","year":"2007","journal-title":"Bioinformatics"},{"key":"2026100119561895000_ref52","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"2026100119561895000_ref53","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","article-title":"HiC-Pro: an optimized and flexible pipeline for Hi-C data processing","volume":"16","author":"Servant","year":"2015","journal-title":"Genome Biol"},{"key":"2026100119561895000_ref54","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: a 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput Sci Eng"},{"key":"2026100119561895000_ref55","doi-asserted-by":"crossref","first-page":"W265","DOI":"10.1093\/nar\/gkm286","article-title":"LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons","volume":"35","author":"Xu","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2026100119561895000_ref56","doi-asserted-by":"crossref","first-page":"i152","DOI":"10.1093\/bioinformatics\/bti1003","article-title":"PILER: identification and classification of genomic repeats","volume":"21","author":"Edgar","year":"2005","journal-title":"Bioinformatics"},{"key":"2026100119561895000_ref57","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2026100119561895000_ref58","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol"},{"key":"2026100119561895000_ref59","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1186\/1471-2164-7-327","article-title":"Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis","volume":"7","author":"Campbell","year":"2006","journal-title":"BMC Genomics"},{"key":"2026100119561895000_ref60","doi-asserted-by":"crossref","first-page":"D471","DOI":"10.1093\/nar\/gkn661","article-title":"HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB\/Swiss-Prot","volume":"37","author":"Lima","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2026100119561895000_ref61","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2026100119561895000_ref62","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"2026100119561895000_ref63","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gki081","article-title":"Rfam: annotating non-coding RNAs in complete genomes","volume":"33","author":"Griffiths-Jones","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2026100119561895000_ref64","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":"2026100119561895000_ref65","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2026100119561895000_ref66","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":"2026100119561895000_ref67","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1093\/molbev\/msj024","article-title":"Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds","volume":"23","author":"Yang","year":"2005","journal-title":"Mol Biol Evol"},{"key":"2026100119561895000_ref68","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1093\/molbev\/mst100","article-title":"Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3","volume":"30","author":"Han","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2026100119561895000_ref69","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026100119561895000_ref70","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2026100119561895000_ref71","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat Methods"},{"key":"2026100119561895000_ref72","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2026100119561895000_ref73","article-title":"SoNAC72-SoMYB44\/SobHLH130 module contributes to flower color fading via regulating anthocyanin biosynthesis by directly binding to the SoUFGT1 promoter in lilac (Syringa oblata)","volume":"12","author":"Wang","year":"2025","journal-title":"Hortic Res"},{"key":"2026100119561895000_ref74","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/s11295-025-01715-8","article-title":"Transcriptome and physiological analysis revealed core genes that promote glutathione metabolism in blue honeysuckle in response to freezing stress","volume":"21","author":"Fan","year":"2025","journal-title":"Tree Genet Genomes"}],"container-title":["Horticulture Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/hr\/advance-article-pdf\/doi\/10.1093\/hr\/uhag198\/68348848\/uhag198.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/13\/10\/uhag198\/68348848\/uhag198.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/13\/10\/uhag198\/68348848\/uhag198.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T23:56:34Z","timestamp":1790898994000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hr\/article\/doi\/10.1093\/hr\/uhag198\/8688524"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,20]]},"references-count":74,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/hr\/uhag198","relation":{},"ISSN":["2052-7276"],"issn-type":[{"value":"2052-7276","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,5,20]]},"article-number":"uhag198"}}