{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T16:23:44Z","timestamp":1787243024995,"version":"build-2736575974"},"reference-count":54,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T00:00:00Z","timestamp":1765411200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42376219"],"award-info":[{"award-number":["42376219"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["41706137"],"award-info":[{"award-number":["41706137"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen University Excellent Graduate Mentor Team Cultivation Program","award":["SZU2025DSTD021"],"award-info":[{"award-number":["SZU2025DSTD021"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Auxin response factors (ARFs) are crucial components of auxin signaling, playing a vital role in plant growth, development, hormone regulation, and stress responses. Salinity influences plant growth and development; however, Avicennia marina exhibits remarkable salt tolerance. This study analyzed Avicennia marina ARF genes (AmARFs) and their roles in responding to salt and indole-3-acetic acid (IAA) stress. The results indicated that across 5\u201315 days, endogenous IAA and abscisic acid (ABA) levels in A. marina leaves showed significant, time-dependent changes under salt and IAA treatments, with IAA fluctuating around 2.0\u20133.3 \u00b5g g\u22121 FW and ABA rising sharply under combined high-salt + IAA conditions (AS25), reaching up to ~25 \u00b5g g\u22121 FW (p &lt; 0.05). This is the first genome-wide identification of 41 ARF genes in Avicennia marina with expression responses to combined salt and auxin treatments. We identified 41 AmARF genes spread across 23 chromosomes. These genes are divided into four groups according to their phylogenetic relationships. Their coding regions encode amino acids from 361 to 1264, and the number of exons varies from 2 to an unspecified upper limit of 25. Examining these gene promoters revealed various hormone- and stress-response elements, with each gene containing distinct response elements. Sixteen miRNAs can inhibit various ARF genes, while protein\u2013protein interactions and 3D structures offered valuable insights into AmARF proteins. GO enrichment analysis revealed that all 41 AmARFs are involved in the auxin-activated signaling pathway and are also involved in cell division. According to the expression experiments, 11 randomly selected genes showed predominantly upregulation in response to salt and IAA stressors compared with controls. These findings extend our understanding of the functional roles of AmARFs in stress responses. The systematic annotation of AmARF family genes offers candidate genes for future functional validation, which may help elucidate the precise roles of AmARFs in stress responses.<\/jats:p>","DOI":"10.3390\/biology14121774","type":"journal-article","created":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T15:43:43Z","timestamp":1765467823000},"page":"1774","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genome-Wide Discovery and Characterization of the Auxin Response Factor (ARF) Gene Family in Avicennia marina That Regulates Phytohormone Levels and Responds to Salt and Auxin Treatments"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6340-8482","authenticated-orcid":false,"given":"Quaid","family":"Hussain","sequence":"first","affiliation":[{"name":"Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of High-Efficiency Utilization of Light in Plants, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China"},{"name":"College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Azhar","family":"Hussain","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of High-Efficiency Utilization of Light in Plants, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China"},{"name":"College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingying","family":"Li","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of High-Efficiency Utilization of Light in Plants, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of High-Efficiency Utilization of Light in Plants, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7690-4781","authenticated-orcid":false,"given":"Chenjing","family":"Shang","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of High-Efficiency Utilization of Light in Plants, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mostafa A.","family":"Abdel-Maksoud","sequence":"additional","affiliation":[{"name":"Research Chair of Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salman","family":"Alrokayan","sequence":"additional","affiliation":[{"name":"Research Chair of Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3942-5455","authenticated-orcid":false,"given":"Abdulaziz","family":"Alamri","sequence":"additional","affiliation":[{"name":"Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1007\/s00425-022-03916-0","article-title":"The Genome of a Mangrove Plant, Avicennia marina, Provides Insights into Adaptation to Coastal Intertidal Habitats","volume":"256","author":"Ma","year":"2022","journal-title":"Planta"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2349","DOI":"10.1111\/tpj.16921","article-title":"Trehalose along with ABA Promotes the Salt Tolerance of Avicennia marina by Regulating Na+ Transport","volume":"119","author":"Song","year":"2024","journal-title":"Plant J."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/s42003-021-02384-8","article-title":"A Reference-Grade Genome Identifies Salt-Tolerance Genes from the Salt-Secreting Mangrove Species Avicennia marina","volume":"4","author":"Natarajan","year":"2021","journal-title":"Commun. 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