A tail of two pandas— Whole Genome K-mer Signature Analysis of the Red Panda (Ailurus fulgens) and the Giant Panda (Ailuropoda melanoleuca) 

A tail of two pandas— Whole Genome K-mer Signature Analysis of the Red Panda (Ailurus fulgens) and the Giant Panda (Ailuropoda melanoleuca)  | 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 A tail of two pandas— Whole Genome K-mer Signature Analysis of the Red Panda ( Ailurus fulgens ) and the Giant Panda ( Ailuropoda melanoleuca ) Matyas Cserhati This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-29891/v2 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 01 Apr, 2021 Read the published version in BMC Genomics → Version 2 posted 7 You are reading this latest preprint version Show more versions Abstract Background : The red panda ( Ailurus fulgens ) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results : A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids as well as A. fulgens were also aligned to draw further phylogenetic inferences. The results from the whole genome study show that A. fulgens is a member of the mustelid clade (p = 9·10 -97 ). A. fulgens also separates from the mephitid Spilogala gracilis . The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens , together with other ursids (p = 1.2·10 -62 ). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study based on the sequence identity matrix seem to place A. fulgens into its own group. Conclusions : The main conclusion that we can draw from this study is that on a whole genome level A. fulgens belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. The mitochondrial results could be due to differing mutational pressures compared to the nucleus. It cannot be said for sure, but it is likely that A. fulgens belongs to the mustelid clade. Epigenetics & Genomics red panda giant panda whole genome k-mer signature Pearson correlation mustelid ursid procyonid mephitid Figures Figure 1 Figure 2 Figure 3 Figure 4 Full Text Supplementary Files SFig1.tiff Supplementary Figure 1. Silhouette plot for three clusters from the WGKS analysis. The average silhouette width is 0.82. SFig2.tiff Supplementary Figure 2. Silhouette plot for four clusters. The average silhouette width is 0.8. SFig3.tiff Supplementary Figure 3. Plot showing the mean silhouette width according to the number of clusters for the mitochondrial data, based on the ‘silhouette’ method. The maximum average silhouette width is 0.51 for two clusters. AdditionalFile1.xlsx Additional File 1: Results of whole genome analysis of 28 species. The files includes a list of species, and the genome sequence files downloaded from NCBI, the PCC matrix which is a result of the WGKS algorithm, as well as the species clusters and the cluster statistics. AdditionalFile2.xlsx Additional File 2: Results of the alignment of mitochondrial DNA from 52 carnivore species. This file includes a species list, the sequence identity matrix, species clustering information and cluster statistics. Cite Share Download PDF Status: Published Journal Publication published 01 Apr, 2021 Read the published version in BMC Genomics → Version 2 posted Editorial decision: Minor revision 07 Feb, 2021 Review # 1 received at journal 19 Nov, 2020 Editor assigned by journal 17 Nov, 2020 Reviewers invited by journal 17 Nov, 2020 Reviewer # 1 agreed at journal 17 Nov, 2020 Submission checks completed at journal 17 Nov, 2020 Editor invited by journal 17 Nov, 2020 You are reading this latest preprint version Show more versions 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-29891","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research article","associatedPublications":[],"authors":[{"id":5101549,"identity":"db4fb24a-23af-4978-862d-b80a26981af1","order_by":0,"name":"Matyas Cserhati","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAyElEQVRIiWNgGAWjYPACCR5+EJVQQKyGAwwSMpINIC0GxGthsDE4AGIRo4W//3Ti549tFjzG51cnfnhgwCDPL3YAvxaJG7mbJQ62SfCY3Xi7WQLoMMOZsxPwazGQ4N0A1XJ2A0hLgsFtQlr4z27+AdJiPAPIIE4LQ+42sC0G/L3biLMF6JdtFmfOSfBI3ODdZpFgIEHYL/z9ZzffqCirswcxbv6osJHnlyagBQwY2UD2gVVKEKEcDP6A7DtArOpRMApGwSgYaQAADMpENgpcj3EAAAAASUVORK5CYII=","orcid":"","institution":"independent scholar","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Matyas","middleName":"","lastName":"Cserhati","suffix":""}],"badges":[],"createdAt":"2020-05-19 05:17:12","currentVersionCode":2,"declarations":"","doi":"10.21203/rs.3.rs-29891/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-29891/v2","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12864-021-07531-3","type":"published","date":"2021-04-01T19:10:49+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":3957017,"identity":"6069c48b-2cf9-429f-8602-286be1f0bebc","added_by":"auto","created_at":"2020-12-02 17:00:04","extension":"jpeg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":2360394,"visible":true,"origin":"","legend":"Heatmap depicting group relationships for 28 species based on results from the WGKS algorithm. Brighter colors represent species pairs which are in the same group, with a PCC value closer to 1. Darker colors represent species pairs which are in different group, with a PCC less than 1.","description":"","filename":"Fig1.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/05d1ec1e9f71cfce6ce48098.jpeg"},{"id":3957019,"identity":"959da17c-2ad3-40ba-a71c-1efd0e8a04f2","added_by":"auto","created_at":"2020-12-02 17:00:04","extension":"tiff","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1478295,"visible":true,"origin":"","legend":"UPGMA-based hierarchical tree for the 28 species based on PCC values. Ursids, felids, and mustelids form separate clades, with S. gracilis in its own group.","description":"","filename":"Fig2.tiff","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/a403b52ac939a9b28aec05f0.tiff"},{"id":3957021,"identity":"f5dd2581-9ba9-404b-9604-8ca2a4c1330a","added_by":"auto","created_at":"2020-12-02 17:00:05","extension":"tiff","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1637802,"visible":true,"origin":"","legend":"Heatmap depicting group relationships for 52 carnivore species based on alignment of the mitochondrial genome using the online MUSCLE software. Brighter colors represent species pairs which are in the same group, with a sequence identity closer to 1. Darker colors represent species pairs which are in different group, with a sequence identity closer to 0.","description":"","filename":"Fig3.tiff","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/84daf404a79c706e84cc5be3.tiff"},{"id":3957023,"identity":"fa6bfde9-2f2e-4639-8a99-22b795274547","added_by":"auto","created_at":"2020-12-02 17:00:05","extension":"tiff","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":3416047,"visible":true,"origin":"","legend":"UPGMA-based hierarchical tree for the 52 species analyzed in the mtDNA study, based on sequence identity metrics. Mustelids and ursids form two large clades, and mephitids, procyonids forming two small groups. 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Silhouette plot for three clusters from the WGKS analysis. The average silhouette width is 0.82.","description":"","filename":"SFig1.tiff","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/8d3e31c2f68ea094bc8a1bb9.tiff"},{"id":3957018,"identity":"43461b43-83b4-4096-ba4d-ec4a134dfb0c","added_by":"auto","created_at":"2020-12-02 17:00:04","extension":"tiff","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":144018,"visible":true,"origin":"","legend":"Supplementary Figure 2. Silhouette plot for four clusters. The average silhouette width is 0.8.","description":"","filename":"SFig2.tiff","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/86ad8959010fdbd2cbfc1f8d.tiff"},{"id":3957020,"identity":"d23606d6-3891-47d2-867b-996dd1f586e3","added_by":"auto","created_at":"2020-12-02 17:00:04","extension":"tiff","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":750140,"visible":true,"origin":"","legend":"Supplementary Figure 3. Plot showing the mean silhouette width according to the number of clusters for the mitochondrial data, based on the ‘silhouette’ method. The maximum average silhouette width is 0.51 for two clusters.","description":"","filename":"SFig3.tiff","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/9eab6f09f22f26f73b6ca197.tiff"},{"id":3957022,"identity":"87e4454a-2c75-4dd5-b0e7-f269d4d1da6a","added_by":"auto","created_at":"2020-12-02 17:00:05","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":25349,"visible":true,"origin":"","legend":"Additional File 1: Results of whole genome analysis of 28 species. The files includes a list of species, and the genome sequence files downloaded from NCBI, the PCC matrix which is a result of the WGKS algorithm, as well as the species clusters and the cluster statistics.","description":"","filename":"AdditionalFile1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/aa4a5ffe683bda7563afea57.xlsx"},{"id":3957024,"identity":"e3a75ca4-4968-4587-a12a-06c15965ffca","added_by":"auto","created_at":"2020-12-02 17:00:05","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":27885,"visible":true,"origin":"","legend":"Additional File 2: Results of the alignment of mitochondrial DNA from 52 carnivore species. This file includes a species list, the sequence identity matrix, species clustering information and cluster statistics.","description":"","filename":"AdditionalFile2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-29891/v2/f6e1f57d11b628e2d687294f.xlsx"}],"financialInterests":"","formattedTitle":"\u003cp\u003eA tail of two pandas— Whole Genome K-mer Signature Analysis of the Red Panda (\u003cem\u003eAilurus fulgens\u003c/em\u003e) and the Giant Panda (\u003cem\u003eAiluropoda melanoleuca\u003c/em\u003e)\u0026nbsp;\u003c/p\u003e","fulltext":[{"header":"Full Text","content":"\u003cp\u003eThis preprint is available for \u003ca href='/article/rs-29891/latest.pdf' target='_blank'\u003edownload as a PDF\u003c/a\u003e.\u003c/p\u003e"}],"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":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"red panda, giant panda, whole genome k-mer signature, Pearson correlation, mustelid, ursid, procyonid, mephitid","lastPublishedDoi":"10.21203/rs.3.rs-29891/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-29891/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e: The red panda (\u003cem\u003eAilurus fulgens\u003c/em\u003e) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. \u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e: A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including \u003cem\u003eA. fulgens\u003c/em\u003e and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids as well as \u003cem\u003eA. fulgens\u003c/em\u003e were also aligned to draw further phylogenetic inferences. \u003c/p\u003e\u003cp\u003eThe results from the whole genome study show that \u003cem\u003eA. fulgens\u003c/em\u003e is a member of the mustelid clade (p = 9·10\u003csup\u003e-97\u003c/sup\u003e). \u003cem\u003eA. fulgens\u003c/em\u003e also separates from the mephitid \u003cem\u003eSpilogala gracilis\u003c/em\u003e. The giant panda, \u003cem\u003eAiluropoda melanoleuca\u003c/em\u003e also clusters away from \u003cem\u003eA. fulgens\u003c/em\u003e, together with other ursids (p = 1.2·10\u003csup\u003e-62\u003c/sup\u003e). This could be due to the geographic isolation of \u003cem\u003eA. fulgens\u003c/em\u003e from other mustelid species. However, results from the mitochondrial study based on the sequence identity matrix seem to place \u003cem\u003eA. fulgens\u003c/em\u003e into its own group.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e: The main conclusion that we can draw from this study is that on a whole genome level \u003cem\u003eA. fulgens\u003c/em\u003e belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified \u003cem\u003eA. fulgens\u003c/em\u003e and \u003cem\u003eA. melanoleuca\u003c/em\u003e as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. The mitochondrial results could be due to differing mutational pressures compared to the nucleus. It cannot be said for sure, but it is likely that \u003cem\u003eA. fulgens\u003c/em\u003e belongs to the mustelid clade.\u003c/p\u003e","manuscriptTitle":"A tail of two pandas— Whole Genome K-mer Signature Analysis of the Red Panda (Ailurus fulgens) and the Giant Panda (Ailuropoda melanoleuca)\u0026nbsp;","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2020-12-02 17:00:02","doi":"10.21203/rs.3.rs-29891/v2","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Minor revision","date":"2021-02-08T00:00:00+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2020-11-20T00:00:00+00:00","index":1,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"editorAssigned","content":"","date":"2020-11-18T00:00:00+00:00","index":"","fulltext":""},{"type":"reviewersInvited","content":"","date":"2020-11-18T00:00:00+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-11-18T00:00:00+00:00","index":1,"fulltext":""},{"type":"checksComplete","content":"","date":"2020-11-17T23:00:00+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2020-11-17T23:00:00+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2020-05-26 23:03:12","doi":"10.21203/rs.3.rs-29891/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Major revision","date":"2020-10-24T12:00:00+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2020-10-22T12:00:00+00:00","index":2,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"reviewerAgreed","content":"","date":"2020-09-06T12:00:00+00:00","index":2,"fulltext":""},{"type":"editorInvitedReview","content":"","date":"2020-07-03T12:00:00+00:00","index":1,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"reviewerAgreed","content":"","date":"2020-06-10T12:00:00+00:00","index":1,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2020-06-09T12:00:00+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2020-05-19T12:00:00+00:00","index":"","fulltext":""},{"type":"submitted","content":"","date":"2020-05-18T12:00:00+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2020-05-18T12:00:00+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2020-05-18T12:00:00+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"d4bf6e01-1830-41e1-b8c8-c850e8f21127","owner":[],"postedDate":"December 2nd, 2020","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":1298724,"name":"Epigenetics \u0026 Genomics"}],"tags":[],"updatedAt":"2021-08-18T19:43:08+00:00","versionOfRecord":{"articleIdentity":"rs-29891","link":"https://doi.org/10.1186/s12864-021-07531-3","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2021-04-01 19:10:49","publishedOnDateReadable":"April 1st, 2021"},"versionCreatedAt":"2020-12-02 17:00:02","video":"","vorDoi":"10.1186/s12864-021-07531-3","vorDoiUrl":"https://doi.org/10.1186/s12864-021-07531-3","workflowStages":[]},"version":"v2","identity":"rs-29891","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-29891","identity":"rs-29891","version":["v2"]},"buildId":"7rjqhiLT3MXkJMwkYKINL","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}