Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta

Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta | 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 Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta Huinan Li, Lili Liu, Zuyang Qiu, Fanglian He, Weiqing Dong This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4340095/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 17 Jan, 2025 Read the published version in BMC Plant Biology → Version 1 posted 9 You are reading this latest preprint version Abstract Colocasia esculenta ranks as the fifth most important tuber crop and is known for its high nutritional and medicinal value. However, there is no research on its mitochondrial genome, hindering in-depth exploration of its genomic resources and genetic relationships. Using second- and third-generation sequencing technologies, we assembled and annotated the mitogenome of C. esculenta . Its mitogenome mainly consists of five circular DNA molecules, with a total length of 594,811 bp and a GC content of 46.25%. A total of 55 genes, 157 simple sequence repeats, 29 tandem repeat sequences, 202 dispersed repeat sequences, and 625 RNA editing sites were detected. Most protein-coding genes use ATG as the start codon, and the third position of the codon tends to be A or T (U). GAA, AUU, and UUU are the most common codons in C. esculenta mitochondria. Finally, based on 28 representative plant species, a phylogenetic tree was constructed, revealing a close relationship between C. esculenta and Araceae . This study provides comprehensive information on C. esculenta , laying a foundation for crop genetics and molecular breeding. Colocasia esculenta Mitochondrial Genome Comparative Analysis Phylogenetic Relationships Repeat Sequence Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 17 Jan, 2025 Read the published version in BMC Plant Biology → Version 1 posted Editorial decision: Revision requested 06 Nov, 2024 Reviews received at journal 03 Nov, 2024 Reviewers agreed at journal 14 Oct, 2024 Reviews received at journal 27 May, 2024 Reviewers agreed at journal 10 May, 2024 Reviewers invited by journal 07 May, 2024 Editor assigned by journal 06 May, 2024 Submission checks completed at journal 06 May, 2024 First submitted to journal 28 Apr, 2024 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. 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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-4340095","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":299942656,"identity":"c3382803-00d6-482a-b798-0c2bc8cb2fff","order_by":0,"name":"Huinan Li","email":"","orcid":"","institution":"Guangxi Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Huinan","middleName":"","lastName":"Li","suffix":""},{"id":299942660,"identity":"4cca4e3a-9592-41f2-952b-afab3819606a","order_by":1,"name":"Lili Liu","email":"","orcid":"","institution":"Lipu City Agricultural and Rural Bureau","correspondingAuthor":false,"prefix":"","firstName":"Lili","middleName":"","lastName":"Liu","suffix":""},{"id":299942664,"identity":"4529ba89-2534-4bc0-a813-8d9d757ffd31","order_by":2,"name":"Zuyang Qiu","email":"","orcid":"","institution":"Lipu City Agricultural and Rural Bureau","correspondingAuthor":false,"prefix":"","firstName":"Zuyang","middleName":"","lastName":"Qiu","suffix":""},{"id":299942667,"identity":"8ecd02f7-f2ca-44cd-92c0-e142aac44e11","order_by":3,"name":"Fanglian He","email":"","orcid":"","institution":"Guangxi Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Fanglian","middleName":"","lastName":"He","suffix":""},{"id":299942669,"identity":"51807858-dd16-4504-a6ff-8da9f4f401f4","order_by":4,"name":"Weiqing Dong","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA9ElEQVRIiWNgGAWjYDCCA2BSgoGNgYHxAclamA3QRPFqAQM2CaK08B3vPfyap8JCtk+6/Vrl1zY7efkG3oOPP+DRInnmXJo1zxkJ4zaZM2W3Zc4kG244wJdsgM8Wgxs5Zsa5bRKJbRI5abclKpgZNzDwmEkQ1vIPoqVYwqDefn4Dj/kPAlqMH+c2gLSkH2P8UHE4seEAjxle70ueOWPG/OcY0C8SOczSDGeOJ284zGMscQaPFr7jPcYfZ9TUyc6fkf7w48+2atv57T2GHyrwaGGARgdjAwOPATMPiM+MXzlYyQeIFvYHjD8Iqx4Fo2AUjIIRCABe41KE2fl04wAAAABJRU5ErkJggg==","orcid":"","institution":"Guangxi Academy of Agricultural Sciences","correspondingAuthor":true,"prefix":"","firstName":"Weiqing","middleName":"","lastName":"Dong","suffix":""}],"badges":[],"createdAt":"2024-04-29 04:01:49","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4340095/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4340095/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12870-025-06082-z","type":"published","date":"2025-01-17T15:56:55+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":74284455,"identity":"23480e50-5ac8-4e10-88fa-394bffa288fe","added_by":"auto","created_at":"2025-01-20 16:05:59","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1263377,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4340095/v1_covered_4093fee2-8306-4bd7-bc22-2371b6bd507d.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta","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":"Colocasia esculenta, Mitochondrial Genome, Comparative Analysis, Phylogenetic Relationships, Repeat Sequence","lastPublishedDoi":"10.21203/rs.3.rs-4340095/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4340095/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e \u003cem\u003eColocasia esculenta\u003c/em\u003e ranks as the fifth most important tuber crop and is known for its high nutritional and medicinal value. However, there is no research on its mitochondrial genome, hindering in-depth exploration of its genomic resources and genetic relationships. Using second- and third-generation sequencing technologies, we assembled and annotated the mitogenome of \u003cem\u003eC. esculenta\u003c/em\u003e. Its mitogenome mainly consists of five circular DNA molecules, with a total length of 594,811 bp and a GC content of 46.25%. A total of 55 genes, 157 simple sequence repeats, 29 tandem repeat sequences, 202 dispersed repeat sequences, and 625 RNA editing sites were detected. Most protein-coding genes use ATG as the start codon, and the third position of the codon tends to be A or T (U). GAA, AUU, and UUU are the most common codons in \u003cem\u003eC. esculenta\u003c/em\u003e mitochondria. Finally, based on 28 representative plant species, a phylogenetic tree was constructed, revealing a close relationship between \u003cem\u003eC. esculenta\u003c/em\u003e and \u003cem\u003eAraceae\u003c/em\u003e. This study provides comprehensive information on \u003cem\u003eC. esculenta\u003c/em\u003e, laying a foundation for crop genetics and molecular breeding.\u003c/p\u003e","manuscriptTitle":"Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-05-10 05:34:46","doi":"10.21203/rs.3.rs-4340095/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-11-06T21:26:39+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-11-03T14:13:32+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"94779410419538653788919404832808941021","date":"2024-10-15T03:43:04+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-05-27T10:58:34+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"114020596545283104791660420018122230456","date":"2024-05-10T04:26:48+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-05-08T01:32:28+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-05-06T11:30:56+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-05-06T11:30:37+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2024-04-29T03:59:09+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":"a43cce6e-29cd-45ab-a6e1-ebe5a2ae0b5b","owner":[],"postedDate":"May 10th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-01-20T15:58:46+00:00","versionOfRecord":{"articleIdentity":"rs-4340095","link":"https://doi.org/10.1186/s12870-025-06082-z","journal":{"identity":"bmc-plant-biology","isVorOnly":false,"title":"BMC Plant Biology"},"publishedOn":"2025-01-17 15:56:55","publishedOnDateReadable":"January 17th, 2025"},"versionCreatedAt":"2024-05-10 05:34:46","video":"","vorDoi":"10.1186/s12870-025-06082-z","vorDoiUrl":"https://doi.org/10.1186/s12870-025-06082-z","workflowStages":[]},"version":"v1","identity":"rs-4340095","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4340095","identity":"rs-4340095","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}