In silico identification of auxin-responsive genes through de novo transcriptome assembly and differential expression analysis during early adventitious root formation in contrasting genotypes of Melia dubia Cav

In silico identification of auxin-responsive genes through de novo transcriptome assembly and differential expression analysis during early adventitious root formation in contrasting genotypes of Melia dubia Cav | 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 In silico identification of auxin-responsive genes through de novo transcriptome assembly and differential expression analysis during early adventitious root formation in contrasting genotypes of Melia dubia Cav Aghila Samji, Komal Eashwarlal, Krishnan Shanthi, Rekha R Warrier This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8823167/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 10 You are reading this latest preprint version Abstract This study investigates the molecular basis of auxin-induced adventitious root (AR) formation in Melia dubia Cav., a commercially important tree species. Juvenile stem cuttings from a good rooter (MG) and a poor rooter (MP) were pulse-treated with indole-3-butyric acid (IBA), and basal tissues were sampled at 0, 12, 24, and 36 hours for RNA sequencing. De novo assembly of RNA-seq data yielded 94,337 and 79,103 unigenes for MG and MP, respectively. Functional annotation against NCBI, KEGG, COG, and GO databases revealed enrichment of hormone signal transduction pathways, metabolic processes, and secondary metabolite biosynthesis. Although MP exhibited a higher number of differentially expressed genes, MG showed earlier, coordinated, and pathway-specific activation, particularly in auxin-related signaling. AUX1/LAX influx carriers, TIR1/AFB receptors, AUX/IAA repressors, ARF transcription factors, GH3, and SAUR gene families—were more extensively and temporally regulated in MG. Positive regulators such as ARF7, ARF19, GH3-1, and several SAUR genes were preferentially expressed in the good-rooting genotype. KEGG enrichment highlighted plant hormone signal transduction, flavonoid biosynthesis, and ABC transporter pathways as central to efficient AR formation. Overall, superior rooting in M.dubia is associated with precise temporal regulation of auxin signalling and transport, providing molecular insights and potential markers for improving clonal propagation. Auxin signalling RNA -seq Clonal propagation Differential gene expression ARF transcription factors Hormone signal transduction Flavonoid biosynthesis Full Text Additional Declarations No competing interests reported. Table 1 to 3 are available in the Supplementary Files section. Supplementary Files Supplementarytable.xlsx 4.Tables.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 13 Apr, 2026 Reviews received at journal 05 Apr, 2026 Reviewers agreed at journal 04 Apr, 2026 Reviewers agreed at journal 04 Apr, 2026 Reviewers agreed at journal 19 Mar, 2026 Reviewers invited by journal 18 Mar, 2026 Editor invited by journal 25 Feb, 2026 Editor assigned by journal 23 Feb, 2026 Submission checks completed at journal 21 Feb, 2026 First submitted to journal 21 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-8823167","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":608889201,"identity":"a0b85a62-2870-4255-90ae-3e911c6fdc6a","order_by":0,"name":"Aghila Samji","email":"","orcid":"","institution":"Institute of Forest Genetics and Tree Breeding","correspondingAuthor":false,"prefix":"","firstName":"Aghila","middleName":"","lastName":"Samji","suffix":""},{"id":608889202,"identity":"3ec4ca53-4296-49e3-a3b7-bf2eac32b7c4","order_by":1,"name":"Komal Eashwarlal","email":"","orcid":"","institution":"Institute of Forest Genetics and Tree 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Juvenile stem cuttings from a good rooter (MG) and a poor rooter (MP) were pulse-treated with indole-3-butyric acid (IBA), and basal tissues were sampled at 0, 12, 24, and 36 hours for RNA sequencing. De novo assembly of RNA-seq data yielded 94,337 and 79,103 unigenes for MG and MP, respectively. Functional annotation against NCBI, KEGG, COG, and GO databases revealed enrichment of hormone signal transduction pathways, metabolic processes, and secondary metabolite biosynthesis. Although MP exhibited a higher number of differentially expressed genes, MG showed earlier, coordinated, and pathway-specific activation, particularly in auxin-related signaling. AUX1/LAX influx carriers, TIR1/AFB receptors, AUX/IAA repressors, ARF transcription factors, GH3, and SAUR gene families\u0026mdash;were more extensively and temporally regulated in MG. Positive regulators such as ARF7, ARF19, GH3-1, and several SAUR genes were preferentially expressed in the good-rooting genotype. 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