{"id":"https://openalex.org/W7225827462","doi":"https://doi.org/10.3390/ijms272210122","title":"Comparative Analysis of Chloroplast Genomes and New Insights into the Phylogenetic Relationships of Lycoris","display_name":"Comparative Analysis of Chloroplast Genomes and New Insights into the Phylogenetic Relationships of Lycoris","publication_year":2026,"publication_date":"2026-11-11","ids":{"openalex":"https://openalex.org/W7225827462","doi":"https://doi.org/10.3390/ijms272210122"},"language":"en","primary_location":{"id":"doi:10.3390/ijms272210122","doi":"https://doi.org/10.3390/ijms272210122","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms272210122","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","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":"International Journal of Molecular Sciences","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/ijms272210122","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081712840","display_name":"Lihui Mao","orcid":"https://orcid.org/0000-0002-9556-6642","observed_orcids":["https://orcid.org/0000-0002-9556-6642"]},"institutions":[{"id":"https://openalex.org/I4210126939","display_name":"ZheJiang Academy of Agricultural Sciences","ror":"https://ror.org/02qbc3192","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210126939"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lihui Mao","raw_affiliation_strings":["Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China","institution_ids":["https://openalex.org/I4210126939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114039921","display_name":"Xuerui Cao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210126939","display_name":"ZheJiang Academy of Agricultural Sciences","ror":"https://ror.org/02qbc3192","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210126939"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuerui Cao","raw_affiliation_strings":["Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China","institution_ids":["https://openalex.org/I4210126939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101447944","display_name":"Qing Dong","orcid":"https://orcid.org/0000-0002-1969-2516","observed_orcids":["https://orcid.org/0000-0002-1969-2516"]},"institutions":[{"id":"https://openalex.org/I4210126939","display_name":"ZheJiang Academy of Agricultural Sciences","ror":"https://ror.org/02qbc3192","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210126939"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qing Dong","raw_affiliation_strings":["Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China","institution_ids":["https://openalex.org/I4210126939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101955737","display_name":"Wei Hu","orcid":"https://orcid.org/0000-0003-1589-4310","observed_orcids":["https://orcid.org/0000-0003-1589-4310"]},"institutions":[{"id":"https://openalex.org/I4210126939","display_name":"ZheJiang Academy of Agricultural Sciences","ror":"https://ror.org/02qbc3192","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210126939"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Hu","raw_affiliation_strings":["Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China","institution_ids":["https://openalex.org/I4210126939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110238261","display_name":"Danqing Tian","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210126939","display_name":"ZheJiang Academy of Agricultural Sciences","ror":"https://ror.org/02qbc3192","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210126939"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Danqing Tian","raw_affiliation_strings":["Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China","institution_ids":["https://openalex.org/I4210126939"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064136102","display_name":"Qingcheng Zou","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210126939","display_name":"ZheJiang Academy of Agricultural Sciences","ror":"https://ror.org/02qbc3192","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210126939"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingcheng Zou","raw_affiliation_strings":["Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China","institution_ids":["https://openalex.org/I4210126939"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210126939"],"apc_list":{"value":2900,"currency":"CHF","value_usd":3499},"apc_paid":{"value":2900,"currency":"CHF","value_usd":3499},"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":"27","issue":"22","first_page":"10122","last_page":"10122"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.9854000210762024,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.9854000210762024,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13168","display_name":"Plant Ecology and Taxonomy Studies","score":0.009399999864399433,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.002099999925121665,"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"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9016000032424927},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7914000153541565},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7409999966621399},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5547000169754028},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.49939998984336853},{"id":"https://openalex.org/C157369684","wikidata":"https://www.wikidata.org/wiki/Q34740","display_name":"Genus","level":2,"score":0.4406999945640564},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.4146000146865845},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37929999828338623},{"id":"https://openalex.org/C93829228","wikidata":"https://www.wikidata.org/wiki/Q165963","display_name":"Plastid","level":4,"score":0.36410000920295715},{"id":"https://openalex.org/C58677359","wikidata":"https://www.wikidata.org/wiki/Q7201511","display_name":"Plant evolution","level":4,"score":0.30399999022483826},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.29910001158714294},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.296999990940094},{"id":"https://openalex.org/C141036","wikidata":"https://www.wikidata.org/wiki/Q5158537","display_name":"Concerted evolution","level":4,"score":0.29010000824928284},{"id":"https://openalex.org/C69305403","wikidata":"https://www.wikidata.org/wiki/Q47263","display_name":"Chloroplast","level":3,"score":0.2856999933719635},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.28450000286102295},{"id":"https://openalex.org/C48050816","wikidata":"https://www.wikidata.org/wiki/Q3182853","display_name":"Chloroplast DNA","level":4,"score":0.2782000005245209},{"id":"https://openalex.org/C61271108","wikidata":"https://www.wikidata.org/wiki/Q3180866","display_name":"Genome size","level":4,"score":0.26269999146461487}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3390/ijms272210122","doi":"https://doi.org/10.3390/ijms272210122","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms272210122","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","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":"International Journal of Molecular Sciences","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.3390/ijms272210122","doi":"https://doi.org/10.3390/ijms272210122","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms272210122","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","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":"International Journal of Molecular Sciences","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1956276071","https://openalex.org/W1986364193","https://openalex.org/W2101392937","https://openalex.org/W2111647009","https://openalex.org/W2124281279","https://openalex.org/W2141052558","https://openalex.org/W2160378127","https://openalex.org/W2605276928","https://openalex.org/W2612261225","https://openalex.org/W2614081736","https://openalex.org/W2755331695","https://openalex.org/W2783036180","https://openalex.org/W2801159594","https://openalex.org/W2806753069","https://openalex.org/W2901954177","https://openalex.org/W2912669907","https://openalex.org/W2946296764","https://openalex.org/W2951912016","https://openalex.org/W2998263476","https://openalex.org/W3035612185","https://openalex.org/W3082453057","https://openalex.org/W3085462977","https://openalex.org/W3095204875","https://openalex.org/W3127646330","https://openalex.org/W3202481026","https://openalex.org/W4210459954","https://openalex.org/W4210802361","https://openalex.org/W4210833610","https://openalex.org/W4213385292","https://openalex.org/W4220994049","https://openalex.org/W4223470863","https://openalex.org/W4282033807","https://openalex.org/W4288723768","https://openalex.org/W4313424532","https://openalex.org/W4387940396","https://openalex.org/W4406686366","https://openalex.org/W4407167287","https://openalex.org/W4414159750","https://openalex.org/W4414781196","https://openalex.org/W7161679288"],"related_works":[],"abstract_inverted_index":{"The":[0,67,272],"genus":[1,193],"Lycoris,":[2],"comprising":[3,95],"approximately":[4],"25":[5],"species,":[6],"has":[7],"high":[8],"medicinal":[9],"and":[10,17,23,35,43,64,100,107,128,138,160,196,199,225,229,257,269,303,309],"ornamental":[11],"value.":[12],"However,":[13],"frequent":[14],"interspecific":[15],"hybridization":[16,228],"polyploidization":[18],"have":[19],"complicated":[20],"species":[21,36,149,221,239],"delimitation":[22],"germplasm":[24],"identification.":[25,37],"Complete":[26],"chloroplast":[27,47,93,299],"genomes":[28,48,118],"are":[29,222,317],"widely":[30,161],"used":[31],"for":[32],"phylogenetic":[33],"reconstruction":[34],"In":[38],"this":[39,285],"study,":[40],"we":[41],"sequenced":[42,234],"assembled":[44],"the":[45,120,141,168,171,177,187,192,206,232,236,263],"complete":[46],"of":[49,85,146,170],"L.":[50,52,54,56,58,60,62,65,75,81,250,267,282],"haywardii,":[51],"guangxiensis,":[53],"chunxiaoensis,":[55],"wulingensis,":[57],"tsinlingensis,":[59],"sp.,":[61],"caldwellii,":[63],"hubeiensis.":[66],"genome":[68,126],"sizes":[69],"ranged":[70],"from":[71,242,281],"158,461":[72],"bp":[73,79],"in":[74,80,91,254,262],"wulingensis":[76],"to":[77,136,176,249,319],"158,772":[78],"guangxiensis.":[82],"A":[83],"total":[84],"132":[86],"gene":[87,103,129],"copies":[88,104],"were":[89],"annotated":[90],"each":[92,154],"genome,":[94],"86":[96],"protein-coding,":[97],"38":[98],"tRNA":[99],"eight":[101,117],"rRNA":[102],"(78,":[105],"30":[106],"four":[108,151],"unique":[109,114],"sequences,":[110],"respectively,":[111],"i.e.,":[112],"112":[113],"genes).":[115],"All":[116],"exhibited":[119],"typical":[121],"quadripartite":[122],"structure,":[123],"with":[124,186,214,290,314],"conserved":[125],"organization":[127],"content.":[130],"Size":[131],"variation":[132,305],"was":[133],"mainly":[134,253],"attributable":[135],"expansion":[137],"contraction":[139],"at":[140,194],"IR/SC":[142],"boundaries.":[143],"Phylogenetic":[144],"analysis":[145],"extant":[147],"Lycoris":[148,173,220],"resolved":[150],"major":[152],"clades,":[153],"containing":[155],"one":[156],"or":[157,311],"two":[158,188],"representative":[159],"recognized":[162],"native":[163],"species.":[164],"Divergence-time":[165],"estimation":[166],"dated":[167],"crown":[169],"sampled":[172],"plastid":[174,202],"lineages":[175],"late":[178],"Miocene":[179],"(6.65":[180],"Mya,":[181],"95%":[182],"HPD":[183],"5.73\u20137.67":[184],"Mya),":[185],"deepest":[189],"splits":[190],"within":[191],"6.06":[195],"4.08":[197],"Mya":[198],"most":[200,219],"terminal":[201],"divergences":[203],"occurring":[204],"during":[205],"Pleistocene":[207],"(0.02\u20131.47":[208],"Mya).":[209],"This":[210],"pattern":[211],"is":[212,245],"consistent":[213],"previous":[215],"studies":[216],"suggesting":[217],"that":[218],"evolutionarily":[223],"young":[224],"originated":[226],"through":[227],"polyploidization.":[230],"Among":[231],"newly":[233],"taxa,":[235],"unidentified":[237],"wild":[238],"(L.":[240],"sp.)":[241],"Shaanxi":[243],"Province":[244],"morphologically":[246],"nearly":[247],"identical":[248],"shaanxiensis,":[251,283],"differing":[252],"flower":[255],"color,":[256],"plastome":[258,291],"phylogenies":[259],"place":[260],"it":[261],"same":[264],"clade":[265],"as":[266],"shaanxiensis":[268],"its":[270,321],"allies.":[271],"taxon":[273],"may":[274],"therefore":[275],"represent":[276],"a":[277],"color":[278],"variant":[279],"derived":[280],"but":[284],"hypothesis":[286],"cannot":[287],"be":[288],"tested":[289],"data":[292],"alone:":[293],"recent":[294],"divergence,":[295],"shared":[296],"maternal":[297],"ancestry,":[298],"introgression,":[300],"hybrid":[301],"origin":[302],"intraspecific":[304],"remain":[306],"equally":[307],"plausible,":[308],"nuclear":[310],"genome-wide":[312],"markers":[313],"population-level":[315],"sampling":[316],"needed":[318],"resolve":[320],"status.":[322]},"counts_by_year":[],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2026-11-12T00:00:00"}
