{"id":"https://openalex.org/W7225399396","doi":"https://doi.org/10.3390/biology15212023","title":"Haplotype-Resolved Chromosome-Scale Genome Assembly of Lonicera macranthoides Hand.-Mazz. Reveals Genetic Determinants of Bioactive Compound Biosynthesis and Phytohormone-Mediated Metabolic Regulation","display_name":"Haplotype-Resolved Chromosome-Scale Genome Assembly of Lonicera macranthoides Hand.-Mazz. Reveals Genetic Determinants of Bioactive Compound Biosynthesis and Phytohormone-Mediated Metabolic Regulation","publication_year":2026,"publication_date":"2026-11-06","ids":{"openalex":"https://openalex.org/W7225399396","doi":"https://doi.org/10.3390/biology15212023"},"language":"en","primary_location":{"id":"doi:10.3390/biology15212023","doi":"https://doi.org/10.3390/biology15212023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/biology15212023","pdf_url":null,"source":{"id":"https://openalex.org/S153489431","display_name":"Biology","issn_l":"2079-7737","issn":["2079-7737"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/biology15212023","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038730380","display_name":"Qundong Liu","orcid":"https://orcid.org/0009-0004-6226-6207","observed_orcids":["https://orcid.org/0009-0004-6226-6207"]},"institutions":[{"id":"https://openalex.org/I4210141683","display_name":"China Academy of Chinese Medical Sciences","ror":"https://ror.org/042pgcv68","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210141683"]},{"id":"https://openalex.org/I4210155102","display_name":"Chongqing Academy of Chinese Materia Medica","ror":"https://ror.org/049pz8m51","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210155102"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qundong Liu","raw_affiliation_strings":["China Academy of Chinese Medical Sciences, Beijing 100700, China","Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"China Academy of Chinese Medical Sciences, Beijing 100700, China","institution_ids":["https://openalex.org/I4210141683"]},{"raw_affiliation_string":"Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China","institution_ids":["https://openalex.org/I4210155102"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161086117","display_name":"Xuhong Song","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210155102","display_name":"Chongqing Academy of Chinese Materia Medica","ror":"https://ror.org/049pz8m51","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210155102"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuhong Song","raw_affiliation_strings":["Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China","institution_ids":["https://openalex.org/I4210155102"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025861070","display_name":"Tao Dou","orcid":"https://orcid.org/0000-0003-0161-2263","observed_orcids":["https://orcid.org/0000-0003-0161-2263"]},"institutions":[{"id":"https://openalex.org/I4210155102","display_name":"Chongqing Academy of Chinese Materia Medica","ror":"https://ror.org/049pz8m51","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210155102"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Dou","raw_affiliation_strings":["Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China"],"raw_orcid":"https://orcid.org/0000-0003-0161-2263","affiliations":[{"raw_affiliation_string":"Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China","institution_ids":["https://openalex.org/I4210155102"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049372794","display_name":"Gang Ding","orcid":"https://orcid.org/0000-0002-8178-4788","observed_orcids":["https://orcid.org/0000-0002-8178-4788"]},"institutions":[{"id":"https://openalex.org/I4210155102","display_name":"Chongqing Academy of Chinese Materia Medica","ror":"https://ror.org/049pz8m51","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210155102"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gang Ding","raw_affiliation_strings":["Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China","institution_ids":["https://openalex.org/I4210155102"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016422446","display_name":"\u674e\u9686\u4e91","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210155102","display_name":"Chongqing Academy of Chinese Materia Medica","ror":"https://ror.org/049pz8m51","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210155102"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Longyun Li","raw_affiliation_strings":["Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China","institution_ids":["https://openalex.org/I4210155102"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016422446"],"corresponding_institution_ids":["https://openalex.org/I4210155102"],"apc_list":{"value":2700,"currency":"CHF","value_usd":3258},"apc_paid":{"value":2700,"currency":"CHF","value_usd":3258},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"15","issue":"21","first_page":"2023","last_page":"2023"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.4120999872684479,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.4120999872684479,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11237","display_name":"Plant Gene Expression Analysis","score":0.27730000019073486,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.12710000574588776,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/lonicera-macranthoides","display_name":"Lonicera macranthoides","score":1.0},{"id":"https://openalex.org/keywords/haplotype-resolved-genome-assembly","display_name":"haplotype-resolved genome assembly","score":0.9599999785423279},{"id":"https://openalex.org/keywords/chromosome-scale-genome","display_name":"chromosome-scale genome","score":0.7919999957084656},{"id":"https://openalex.org/keywords/chlorogenic-acid-biosynthesis","display_name":"chlorogenic acid biosynthesis","score":0.9139999747276306},{"id":"https://openalex.org/keywords/triterpenoid-saponins","display_name":"triterpenoid saponins","score":0.9810000061988831},{"id":"https://openalex.org/keywords/jasmonic-acid","display_name":"jasmonic acid","score":0.9679999947547913},{"id":"https://openalex.org/keywords/isopentenyladenine","display_name":"isopentenyladenine","score":0.9649999737739563},{"id":"https://openalex.org/keywords/floral-organ-development","display_name":"floral organ development","score":0.878000020980835},{"id":"https://openalex.org/keywords/mapk-signaling","display_name":"MAPK signaling","score":0.9919999837875366},{"id":"https://openalex.org/keywords/structural-variants","display_name":"structural variants","score":0.6439999938011169},{"id":"https://openalex.org/keywords/medicinal-plant-genomics","display_name":"medicinal plant genomics","score":0.5950000286102295},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.6779999732971191}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9049999713897705},{"id":"https://openalex.org/C2776559899","wikidata":"https://www.wikidata.org/wiki/Q417181","display_name":"Phenylpropanoid","level":4,"score":0.6820999979972839},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.6506999731063843},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5421000123023987},{"id":"https://openalex.org/C62794011","wikidata":"https://www.wikidata.org/wiki/Q18029694","display_name":"MYB","level":4,"score":0.5375999808311462},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5101000070571899},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4851999878883362},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4697999954223633},{"id":"https://openalex.org/C2781405662","wikidata":"https://www.wikidata.org/wiki/Q207653","display_name":"Triterpenoid saponin","level":4,"score":0.4641999900341034},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.3788999915122986},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.3747999966144562},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3273000121116638},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.323199987411499},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3224000036716461},{"id":"https://openalex.org/C2779311684","wikidata":"https://www.wikidata.org/wiki/Q17774539","display_name":"Bioactive compound","level":2,"score":0.31690001487731934},{"id":"https://openalex.org/C2777347573","wikidata":"https://www.wikidata.org/wiki/Q522244","display_name":"Secondary metabolite","level":3,"score":0.29649999737739563},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.2924000024795532},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.29019999504089355},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.2831999957561493},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2791000008583069},{"id":"https://openalex.org/C22322919","wikidata":"https://www.wikidata.org/wiki/Q5533501","display_name":"Genomic organization","level":4,"score":0.2687000036239624},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.26460000872612},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2590999901294708},{"id":"https://openalex.org/C2779080361","wikidata":"https://www.wikidata.org/wiki/Q415311","display_name":"Jasmonic acid","level":3,"score":0.25850000977516174},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.25609999895095825}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3390/biology15212023","doi":"https://doi.org/10.3390/biology15212023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/biology15212023","pdf_url":null,"source":{"id":"https://openalex.org/S153489431","display_name":"Biology","issn_l":"2079-7737","issn":["2079-7737"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biology","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.3390/biology15212023","doi":"https://doi.org/10.3390/biology15212023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/biology15212023","pdf_url":null,"source":{"id":"https://openalex.org/S153489431","display_name":"Biology","issn_l":"2079-7737","issn":["2079-7737"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323172","display_name":"Natural Science Foundation of Chongqing","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":86,"referenced_works":["https://openalex.org/W1823238691","https://openalex.org/W1999574084","https://openalex.org/W2028536347","https://openalex.org/W2035618305","https://openalex.org/W2036232758","https://openalex.org/W2054254276","https://openalex.org/W2056475163","https://openalex.org/W2061205797","https://openalex.org/W2070287693","https://openalex.org/W2096128575","https://openalex.org/W2101101724","https://openalex.org/W2104956231","https://openalex.org/W2114425137","https://openalex.org/W2116767244","https://openalex.org/W2132141594","https://openalex.org/W2159675211","https://openalex.org/W2169456326","https://openalex.org/W2179438025","https://openalex.org/W2258020595","https://openalex.org/W2293098058","https://openalex.org/W2336300995","https://openalex.org/W2466173816","https://openalex.org/W2481029670","https://openalex.org/W2763539803","https://openalex.org/W2769115673","https://openalex.org/W2772231999","https://openalex.org/W2784788330","https://openalex.org/W2792735481","https://openalex.org/W2793180234","https://openalex.org/W2800857077","https://openalex.org/W2892924790","https://openalex.org/W2910544292","https://openalex.org/W2913207919","https://openalex.org/W2971559821","https://openalex.org/W2991205213","https://openalex.org/W3016984298","https://openalex.org/W3017049640","https://openalex.org/W3043133936","https://openalex.org/W3047598142","https://openalex.org/W3085758516","https://openalex.org/W3092264219","https://openalex.org/W3095522980","https://openalex.org/W3135708842","https://openalex.org/W3157156283","https://openalex.org/W3158541445","https://openalex.org/W3164029006","https://openalex.org/W3210698118","https://openalex.org/W4200530133","https://openalex.org/W4200564640","https://openalex.org/W4210732778","https://openalex.org/W4225166095","https://openalex.org/W4284990903","https://openalex.org/W4304945301","https://openalex.org/W4306818191","https://openalex.org/W4309731127","https://openalex.org/W4321099446","https://openalex.org/W4378172469","https://openalex.org/W4378782439","https://openalex.org/W4384299196","https://openalex.org/W4386143192","https://openalex.org/W4386325519","https://openalex.org/W4388302733","https://openalex.org/W4388726005","https://openalex.org/W4389091144","https://openalex.org/W4391103603","https://openalex.org/W4391401355","https://openalex.org/W4391439086","https://openalex.org/W4392193843","https://openalex.org/W4393164305","https://openalex.org/W4396623218","https://openalex.org/W4396843974","https://openalex.org/W4399185732","https://openalex.org/W4400624089","https://openalex.org/W4402661418","https://openalex.org/W4403010170","https://openalex.org/W4404121027","https://openalex.org/W4405802529","https://openalex.org/W4406777135","https://openalex.org/W4406808336","https://openalex.org/W4409736934","https://openalex.org/W4410186023","https://openalex.org/W4412905218","https://openalex.org/W4414146635","https://openalex.org/W7162518961","https://openalex.org/W7165937593","https://openalex.org/W7166848587"],"related_works":["https://openalex.org/W2336300995","https://openalex.org/W7224124180","https://openalex.org/W3164029006","https://openalex.org/W4378172469","https://openalex.org/W4384299196","https://openalex.org/W4410345936","https://openalex.org/W3157156283","https://openalex.org/W4415968027","https://openalex.org/W7116675233","https://openalex.org/W7165937593"],"abstract_inverted_index":{"Lonicera":[0],"macranthoides":[1],"is":[2],"a":[3,28,109,168],"traditional":[4],"Chinese":[5],"medicinal":[6,24],"herb":[7],"valued":[8],"for":[9,72,152,175],"its":[10],"chlorogenic":[11],"acid":[12,125],"(CGA)":[13],"and":[14,37,57,90,96,104,115,126,134,142,154,171,178],"triterpenoid":[15,86,105],"saponins.":[16],"To":[17],"elucidate":[18],"the":[19,67,73,148],"genetic":[20],"basis":[21],"of":[22],"these":[23],"properties,":[25],"we":[26],"generated":[27],"haplotype-resolved":[29],"chromosome-scale":[30],"genome":[31],"assembly":[32,45],"combining":[33],"PacBio":[34],"long-read":[35],"sequencing":[36],"High-throughput":[38],"Chromosome":[39],"Conformation":[40],"Capture":[41],"(Hi-C)":[42],"data.":[43],"The":[44],"comprises":[46],"two":[47],"haplomes,":[48],"LmacA":[49],"(857.17":[50],"Mb,":[51,60],"contig":[52,61],"N50":[53,62],"=":[54,63],"31.19":[55],"Mb)":[56],"LmacB":[58],"(824.65":[59],"27.17":[64],"Mb),":[65],"representing":[66],"most":[68],"contiguous":[69],"genomic":[70,78,173],"resource":[71],"genus":[74],"to":[75],"date.":[76],"Comparative":[77],"analyses":[79,98],"identified":[80,99],"species-specific":[81],"gene":[82],"families":[83],"enriched":[84],"in":[85,156],"biosynthesis,":[87,107],"phenylpropanoid":[88],"metabolism,":[89],"stress-response":[91],"pathways.":[92],"Integrated":[93],"GWAS,":[94],"transcriptomic,":[95],"metabolomic":[97],"key":[100],"genes":[101],"regulating":[102],"CGA":[103,153],"saponin":[106],"including":[108],"UGT":[110],"cluster,":[111,114],"an":[112],"HCT":[113],"MYB":[116],"transcription":[117,140],"factors.":[118],"We":[119],"further":[120],"found":[121],"evidence":[122],"that":[123],"jasmonic":[124],"isopentenyl":[127],"adenine":[128],"dynamically":[129],"balance":[130],"floral":[131],"organ":[132],"development":[133],"secondary":[135],"metabolite":[136],"accumulation":[137],"via":[138],"MYB/bHLH":[139],"factors":[141],"MAPK":[143],"signaling.":[144],"This":[145],"study":[146],"establishes":[147],"first":[149],"biosynthetic":[150],"pathways":[151],"saponins":[155],"L.":[157],"macranthoides,":[158],"reveals":[159],"regulatory":[160],"mechanisms":[161],"driven":[162],"by":[163],"haplotype":[164],"structural":[165],"variations":[166],"(notably":[167],"Chr7":[169],"inversion),":[170],"provides":[172],"resources":[174],"molecular":[176],"breeding":[177],"bioactive":[179],"compound":[180],"exploitation.":[181]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-11-07T00:00:00"}
