Whole-genome sequencing and analysis of the endophytic fungus Alternaria alternata Y-2 from Leymus chinensis

Whole-genome sequencing and analysis of the endophytic fungus Alternaria alternata Y-2 from Leymus chinensis | 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 Article Whole-genome sequencing and analysis of the endophytic fungus Alternaria alternata Y-2 from Leymus chinensis Feifei Qin, Li Li, Haoyue Chen, Lixia Yang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8612348/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 11 You are reading this latest preprint version Abstract To analyze the auxiliary effect of endophytic fungus Alternaria alternata isolated from Leymus chinensis on the host plant at the genomic level, we isolated this strain of fungus, extracted the genomic DNA and sequenced the whole genome of A. alternata Y-2 on the Illumina Hiseq platform. The raw data was cleaned up using Trimmomatic and checked for quality using FastQC. The sequencing data was assembled using SPAdes, and GeneMark was used to perform gene prediction on the assembly results. The results showed that the genome size of A. alternata Y-2 was 37,383,676 bp, with 51% GC content, and the number of genes encoded was 12,724. A total of 90 tRNAs and 12 rRNAs were predicted. A total of 12627 genes were annotated in the NCBI nucleotide sequences Database, and 21 gene clusters were identifed. The annotation and functional analysis of the complete genome sequence of A. alternata Y-2 provide a theoretical basis for in-depth research on its future development and utilization. Biological sciences/Biotechnology Biological sciences/Computational biology and bioinformatics Biological sciences/Genetics Biological sciences/Microbiology Biological sciences/Molecular biology Biological sciences/Plant sciences Whole genome Endophytic fungus A. alternata Y-2 Development and utilization Related genes Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 13 May, 2026 Reviews received at journal 12 May, 2026 Reviewers agreed at journal 08 May, 2026 Reviews received at journal 17 Apr, 2026 Reviewers agreed at journal 29 Mar, 2026 Reviewers agreed at journal 27 Mar, 2026 Reviewers invited by journal 27 Mar, 2026 Editor assigned by journal 26 Mar, 2026 Editor invited by journal 17 Feb, 2026 Submission checks completed at journal 14 Feb, 2026 First submitted to journal 14 Feb, 2026 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-8612348","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":613944246,"identity":"d6c65645-a2ab-4a79-abf9-1e49e33b3446","order_by":0,"name":"Feifei Qin","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA/UlEQVRIie3PsWrDMBCA4XMFKgXZs41C/AonDAmlQ1/FxmuHdusQXIWAuwS6OhD6GJ5lBOkS8Fro4tIXkLcOHpqMIY3jMYP+8biP4wBstkuMABjAMdBQV415BjaEOAVgBNSnqSi2QwjsCUQAPpvwm3zAvvfhVtI84tjjcsKd92w0vVaOaR9Ok0B7ybxAjOhIpXdPpWa3y5gEq/I0Qc2mPwy7JIe4+lqViqGKKXH7iVh0iC85JJK764xh3QwggBhTP73iriQMP89cCXZkvkQUOdsQUWz0jnwven/x6q2Qvx2G4etb25hZdo91Wpm2h4A6HjmyZ/9/YrPZbLbD/gBriVCIEVRnyQAAAABJRU5ErkJggg==","orcid":"","institution":"Hulunbuir University","correspondingAuthor":true,"prefix":"","firstName":"Feifei","middleName":"","lastName":"Qin","suffix":""},{"id":613944247,"identity":"67d40ad3-2512-4edb-86e2-ff94bbb2d4ce","order_by":1,"name":"Li Li","email":"","orcid":"","institution":"Hulunbuir University","correspondingAuthor":false,"prefix":"","firstName":"Li","middleName":"","lastName":"Li","suffix":""},{"id":613944248,"identity":"4c618a71-0648-4d12-956b-ba7a50f8dfe9","order_by":2,"name":"Haoyue Chen","email":"","orcid":"","institution":"Hulunbuir University","correspondingAuthor":false,"prefix":"","firstName":"Haoyue","middleName":"","lastName":"Chen","suffix":""},{"id":613944249,"identity":"a46dc542-57cd-423d-87ab-65b93f5b2a8b","order_by":3,"name":"Lixia Yang","email":"","orcid":"","institution":"Hulunbuir University","correspondingAuthor":false,"prefix":"","firstName":"Lixia","middleName":"","lastName":"Yang","suffix":""}],"badges":[],"createdAt":"2026-01-15 16:23:31","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8612348/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8612348/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":105752224,"identity":"b0e512b1-fcb4-4bd0-8a54-9536d622ef7d","added_by":"auto","created_at":"2026-03-30 15:56:05","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":977690,"visible":true,"origin":"","legend":"","description":"","filename":"WholegenomesequencingandanalysisoftheendophyticfungusAlternariaalternataY2fromLeymuschinensisminorrevision20260214Finalversion.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8612348/v1_covered_afd29d7e-3716-4f2c-8eed-7763c5500394.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Whole-genome sequencing and analysis of the endophytic fungus Alternaria alternata Y-2 from Leymus chinensis","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"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":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Whole genome, Endophytic fungus, A. alternata Y-2, Development and utilization, Related genes","lastPublishedDoi":"10.21203/rs.3.rs-8612348/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8612348/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eTo analyze the auxiliary effect of endophytic fungus \u003cem\u003eAlternaria alternata\u003c/em\u003e isolated from \u003cem\u003eLeymus chinensis\u003c/em\u003e on the host plant at the genomic level, we isolated this strain of fungus, extracted the genomic DNA and sequenced the whole genome of \u003cem\u003eA. alternata\u003c/em\u003e Y-2 on the Illumina Hiseq platform. 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