Integrating phylogenomic and morphological evidence to solve the taxonomy of Phoebe legendrei (Lauraceae) and closely related species

Integrating phylogenomic and morphological evidence to solve the taxonomy of Phoebe legendrei (Lauraceae) and closely related species | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Integrating phylogenomic and morphological evidence to solve the taxonomy of Phoebe legendrei (Lauraceae) and closely related species Chengyan Shao, Zhi Yang, Yuyu Ye, Jiangbin Lin, Jianyong Lin, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7442734/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 13 Dec, 2025 Read the published version in BMC Plant Biology → Version 1 posted 11 You are reading this latest preprint version Abstract Background The genus Phoebe , belonging to the tribe Perseeae of the Lauraceae, is well known for its important economic value and the need for its conservation. However, the taxonomic delimitation of species remains poorly resolved due to complicated morphological variation in Phoebe , thus hindering conservation efforts and resource utilization. Here we sequenced 18 samples of the genus, reconstructed a new plastome phylogenomic tree of Phoebe from East Asia with special emphasis on Phoebe legendrei and its closely related species. We also conducted comparative analyses of both plastomes and morphology between P. legendrei and its closely related species, and examined the protologue and the type collection of P. legendrei , and conducted a taxonomic treatment. Results Our comparative genomic analysis confirmed that plastomes of the genus Phoebe are relatively conservative, but P. legendrei 94 differs from P. legendrei 143 in number of dispersed repeats, IR boundary, and highly variable regions. The newly reconstructed phylogenomic tree is robustly supported, with Phoebe species divided into three major clades. Phoebe crassipedicella is sister to P. kwangnanensis , but the eight samples of P. legendrei formed two separate subclades (represented by P. legendrei 94 differs from P. legendrei 143, respectively). We conducted a morphological study and revealed that the two subclades differed in perianth lobe size, fruiting pedicel length, and the clasping status of the persistent perianth lobes. We examined the protologue and morphology of the type collection of P. legendrei , and determined a new species, i.e., Phoebe panzhihuaensis sp. nov.. Conclusions In this study, we resolved the taxonomic delimitation within P. legendrei and its closely related species, and discovered a new species of Phoebe from southwestern China. This work contributes to evaluating species diversity within Phoebe and lays the foundation for the conservation and resource utilization of these species. Lauraceae Phoebe panzhihuaensis plastome phylogeny integrative taxonomy Full Text Additional Declarations No competing interests reported. Supplementary Files Additionalfile1.xlsx Additionalfile2.xlsx Cite Share Download PDF Status: Published Journal Publication published 13 Dec, 2025 Read the published version in BMC Plant Biology → Version 1 posted Editorial decision: Revision requested 02 Nov, 2025 Reviews received at journal 27 Oct, 2025 Reviews received at journal 23 Oct, 2025 Reviewers agreed at journal 08 Oct, 2025 Reviewers agreed at journal 08 Oct, 2025 Reviewers agreed at journal 19 Sep, 2025 Reviewers invited by journal 16 Sep, 2025 Editor assigned by journal 16 Sep, 2025 Editor invited by journal 16 Sep, 2025 Submission checks completed at journal 15 Sep, 2025 First submitted to journal 15 Sep, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7442734","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":517450025,"identity":"66034071-69df-464d-b5d0-86c6cb75c426","order_by":0,"name":"Chengyan Shao","email":"","orcid":"","institution":"Nanjing Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Chengyan","middleName":"","lastName":"Shao","suffix":""},{"id":517450026,"identity":"cd7eaf15-6d7c-49ff-8858-66a11d667c34","order_by":1,"name":"Zhi Yang","email":"","orcid":"","institution":"Nanjing Forestry 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species","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Lauraceae, Phoebe panzhihuaensis, plastome, phylogeny, integrative taxonomy","lastPublishedDoi":"10.21203/rs.3.rs-7442734/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7442734/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eThe genus \u003cem\u003ePhoebe\u003c/em\u003e, belonging to the tribe Perseeae of the Lauraceae, is well known for its important economic value and the need for its conservation. However, the taxonomic delimitation of species remains poorly resolved due to complicated morphological variation in \u003cem\u003ePhoebe\u003c/em\u003e, thus hindering conservation efforts and resource utilization. Here we sequenced 18 samples of the genus, reconstructed a new plastome phylogenomic tree of \u003cem\u003ePhoebe\u003c/em\u003e from East Asia with special emphasis on \u003cem\u003ePhoebe legendrei\u003c/em\u003e and its closely related species. We also conducted comparative analyses of both plastomes and morphology between \u003cem\u003eP. legendrei\u003c/em\u003e and its closely related species, and examined the protologue and the type collection of \u003cem\u003eP. legendrei\u003c/em\u003e, and conducted a taxonomic treatment.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eOur comparative genomic analysis confirmed that plastomes of the genus \u003cem\u003ePhoebe\u003c/em\u003e are relatively conservative, but \u003cem\u003eP. legendrei\u003c/em\u003e 94 differs from \u003cem\u003eP. legendrei\u003c/em\u003e 143 in number of dispersed repeats, IR boundary, and highly variable regions. The newly reconstructed phylogenomic tree is robustly supported, with \u003cem\u003ePhoebe\u003c/em\u003e species divided into three major clades. \u003cem\u003ePhoebe crassipedicella\u003c/em\u003e is sister to \u003cem\u003eP. kwangnanensis\u003c/em\u003e, but the eight samples of \u003cem\u003eP. legendrei\u003c/em\u003e formed two separate subclades (represented by \u003cem\u003eP. legendrei\u003c/em\u003e 94 differs from \u003cem\u003eP. legendrei\u003c/em\u003e 143, respectively). We conducted a morphological study and revealed that the two subclades differed in perianth lobe size, fruiting pedicel length, and the clasping status of the persistent perianth lobes. We examined the protologue and morphology of the type collection of \u003cem\u003eP. legendrei\u003c/em\u003e, and determined a new species, i.e., \u003cem\u003ePhoebe panzhihuaensis\u003c/em\u003e sp. nov..\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eIn this study, we resolved the taxonomic delimitation within \u003cem\u003eP. legendrei\u003c/em\u003e and its closely related species, and discovered a new species of \u003cem\u003ePhoebe\u003c/em\u003e from southwestern China. This work contributes to evaluating species diversity within \u003cem\u003ePhoebe\u003c/em\u003e and lays the foundation for the conservation and resource utilization of these species.\u003c/p\u003e","manuscriptTitle":"Integrating phylogenomic and morphological evidence to solve the taxonomy of Phoebe legendrei (Lauraceae) and closely related species","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-24 22:05:26","doi":"10.21203/rs.3.rs-7442734/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-11-02T09:51:57+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-28T00:16:07+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-24T02:03:40+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"25297516517537497081191822469669130885","date":"2025-10-09T03:54:40+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"52501316470857850637453091446969054412","date":"2025-10-09T02:24:42+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"64345227587260708276822165737779835967","date":"2025-09-19T06:30:25+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-16T05:55:15+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-09-16T05:48:09+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-09-16T05:34:34+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-09-16T02:08:28+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2025-09-16T02:05:15+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"0b46d4b4-7e69-44bb-a08a-0b9566f65d46","owner":[],"postedDate":"September 24th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-12-15T16:12:17+00:00","versionOfRecord":{"articleIdentity":"rs-7442734","link":"https://doi.org/10.1186/s12870-025-07929-1","journal":{"identity":"bmc-plant-biology","isVorOnly":false,"title":"BMC Plant Biology"},"publishedOn":"2025-12-13 15:58:54","publishedOnDateReadable":"December 13th, 2025"},"versionCreatedAt":"2025-09-24 22:05:26","video":"","vorDoi":"10.1186/s12870-025-07929-1","vorDoiUrl":"https://doi.org/10.1186/s12870-025-07929-1","workflowStages":[]},"version":"v1","identity":"rs-7442734","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7442734","identity":"rs-7442734","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}