Mitochondrial genomes of Psylloidea (Hemiptera): Highly variable genes, phylogeny and divergence time estimation

Mitochondrial genomes of Psylloidea (Hemiptera): Highly variable genes, phylogeny and divergence time estimation | 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 Mitochondrial genomes of Psylloidea (Hemiptera): Highly variable genes, phylogeny and divergence time estimation Fengnian Wu, Yongqin Zheng, Xueying Wen, Shuyu Peng, Kangyi Deng, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8528597/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Psyllids (Hemiptera: Psylloidea) are recognized as economically important sap-feeders. To enable broad mitogenome recovery, universal long-PCR primers were designed from alignments of 60 published mitogenomes and were validated by benchmarking Sanger-based assemblies against Illumina resequencing across seven species ( Blastopsylla occidentalis , Cornegenapsylla sinica , Macrohomotoma gladiata , Cacopsylla citrisuga , Cacopsylla chinensis , Diaphorina citri , and Bactericera cockerelli ). Single amplicon bands were obtained for each primer set, excepting for multiple bands with the control region (CR) of Diaphorina citri ; each assembly using Sanger sequences was confirmed by Illumina sequencing, independently. Resulting mitogenomes (14,499–15,220 bp) showed high cross-platform concordance, with read depths 193–72,903×. Sliding-window nucleotide diversity across 67 mitogenomes (CR excluded) indicated nad2 , atp8 , nad5 , and nad6 as most variable, whereas cox1 , cox2 , and both rRNAs were most conserved; primer sites lay within low-diversity windows (mean Pi ≤ 0.07). Four lineage-restricted tRNA secondary-structure variants were observed: trnCys , trnGlu , trnGly , trnHis . Phylogenies inferred by maximum likelihood (ML) and Bayesian inference (BI) were largely congruent and resolved family clades as strongly monophyletic; however, the placement of Diaphorina and Diclidophlebia paucipunctata was sensitive to data type, with amino-acid PCG analyses supporting Diaphorina within Psyllidae (Fig. S4) while nucleotide all-gene analyses yielded an alternative Bayesian placement. Relaxed-clock analyses dated crown Psylloidea to the Early Cretaceous (~ 130 Ma; 95% HPD 114–146), with major family divergences concentrated in the Cretaceous (~ 105–98 Ma). This validated workflow expands mitogenomic resources and provides practical marker guidance for barcoded surveillance, pathway inference, and vector risk assessment within integrated pest management. Psylloidea Mitochondrial genome Universal primers Phylogeny Divergence time Integrated pest management Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted 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-8528597","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":572841673,"identity":"6e22f031-a239-4a43-8c01-00f02c73b9a8","order_by":0,"name":"Fengnian Wu","email":"","orcid":"","institution":"Hanshan Normal University","correspondingAuthor":false,"prefix":"","firstName":"Fengnian","middleName":"","lastName":"Wu","suffix":""},{"id":572841674,"identity":"2c271928-2992-4a2d-95f1-dfbb0bc95db4","order_by":1,"name":"Yongqin Zheng","email":"","orcid":"","institution":"Hanshan Normal 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estimation","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Psylloidea, Mitochondrial genome, Universal primers, Phylogeny, Divergence time, Integrated pest management","lastPublishedDoi":"10.21203/rs.3.rs-8528597/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8528597/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003ePsyllids (Hemiptera: Psylloidea) are recognized as economically important sap-feeders. To enable broad mitogenome recovery, universal long-PCR primers were designed from alignments of 60 published mitogenomes and were validated by benchmarking Sanger-based assemblies against Illumina resequencing across seven species (\u003cem\u003eBlastopsylla occidentalis\u003c/em\u003e, \u003cem\u003eCornegenapsylla sinica\u003c/em\u003e, \u003cem\u003eMacrohomotoma gladiata\u003c/em\u003e, \u003cem\u003eCacopsylla citrisuga\u003c/em\u003e, \u003cem\u003eCacopsylla chinensis\u003c/em\u003e, \u003cem\u003eDiaphorina citri\u003c/em\u003e, and \u003cem\u003eBactericera cockerelli\u003c/em\u003e). Single amplicon bands were obtained for each primer set, excepting for multiple bands with the control region (CR) of \u003cem\u003eDiaphorina citri\u003c/em\u003e; each assembly using Sanger sequences was confirmed by Illumina sequencing, independently. Resulting mitogenomes (14,499\u0026ndash;15,220 bp) showed high cross-platform concordance, with read depths 193\u0026ndash;72,903\u0026times;. Sliding-window nucleotide diversity across 67 mitogenomes (CR excluded) indicated \u003cem\u003enad2\u003c/em\u003e, \u003cem\u003eatp8\u003c/em\u003e, \u003cem\u003enad5\u003c/em\u003e, and \u003cem\u003enad6\u003c/em\u003e as most variable, whereas \u003cem\u003ecox1\u003c/em\u003e, \u003cem\u003ecox2\u003c/em\u003e, and both rRNAs were most conserved; primer sites lay within low-diversity windows (mean \u003cem\u003ePi\u003c/em\u003e\u0026thinsp;\u0026le;\u0026thinsp;0.07). Four lineage-restricted tRNA secondary-structure variants were observed: \u003cem\u003etrnCys\u003c/em\u003e, \u003cem\u003etrnGlu\u003c/em\u003e, \u003cem\u003etrnGly\u003c/em\u003e, \u003cem\u003etrnHis\u003c/em\u003e. Phylogenies inferred by maximum likelihood (ML) and Bayesian inference (BI) were largely congruent and resolved family clades as strongly monophyletic; however, the placement of \u003cem\u003eDiaphorina\u003c/em\u003e and \u003cem\u003eDiclidophlebia paucipunctata\u003c/em\u003e was sensitive to data type, with amino-acid PCG analyses supporting \u003cem\u003eDiaphorina\u003c/em\u003e within Psyllidae (Fig. S4) while nucleotide all-gene analyses yielded an alternative Bayesian placement. Relaxed-clock analyses dated crown Psylloidea to the Early Cretaceous (~\u0026thinsp;130 Ma; 95% HPD 114\u0026ndash;146), with major family divergences concentrated in the Cretaceous (~\u0026thinsp;105\u0026ndash;98 Ma). This validated workflow expands mitogenomic resources and provides practical marker guidance for barcoded surveillance, pathway inference, and vector risk assessment within integrated pest management.\u003c/p\u003e","manuscriptTitle":"Mitochondrial genomes of Psylloidea (Hemiptera): Highly variable genes, phylogeny and divergence time estimation","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-13 08:36:51","doi":"10.21203/rs.3.rs-8528597/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"4b04fa06-74cb-4cad-b405-0c282c4ce8ea","owner":[],"postedDate":"January 13th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-01-13T08:36:51+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-13 08:36:51","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8528597","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8528597","identity":"rs-8528597","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}