{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T15:29:53Z","timestamp":1787758193044,"version":"build-2784847793"},"reference-count":40,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Construction of DNA Fingerprint Map for Superior Clones of C. lanceolata","award":["2024R1010006"],"award-info":[{"award-number":["2024R1010006"]}]},{"name":"Department of Human Resources and Social Security, Application of Fast-Growing and High-Quality Clones of C. lanceolata","award":["2024FKJ14"],"award-info":[{"award-number":["2024FKJ14"]}]},{"name":"Identification of Full-Sibling Germplasm from Fourth-Generation Open-Pollinated Progenies of C. lanceolata Using EST-SSR Markers","award":["2023R1052"],"award-info":[{"award-number":["2023R1052"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Cunninghamia lanceolata (Lamb.) Hook. (C. lanceolata) is an important timber tree species in southern China. However, the molecular regulatory mechanisms underlying adventitious root formation during cutting propagation remain largely unclear. The lack of genetic resources has hindered molecular breeding efforts in this species. Methods: In this study, transcriptome analysis was performed on the root systems of scions from elite C. lanceolata clones at 7, 30, and 60 d after cutting. Results: Approximately 69.30 Gb of clean data were obtained. De novo assembly and gene prediction yielded 43,433 protein-coding genes, of which 32,886 (75.7%) were functionally annotated. Temporal clustering and comparative functional enrichment analyses revealed a distinct temporal functional shift during adventitious root development in C. lanceolata. Early stages were dominated by metabolic processes such as pyrimidine metabolism and carbohydrate biosynthesis, whereas later stages were governed by phytohormone signal transduction. Key components of the auxin pathway, including AUX1, AFB, IAA, and SAUR, exhibited dynamic and differential expression, which may be associated with adventitious root growth. Based on the transcriptome data, we identified nine members of the PIN gene family. Both transcriptomic expression profiles and qRT-PCR validation demonstrated that these PIN genes showed divergent expression trends across developmental stages, suggesting that they may participate in rooting by regulating polar auxin transport. Conclusions: This study systematically elucidates the molecular network underlying adventitious root formation in C. lanceolata cuttings. It enriches the omics resources for conifers and provides a theoretical foundation and omics basis for molecular breeding and efficient propagation of elite C. lanceolata clones.<\/jats:p>","DOI":"10.3390\/genes17091008","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T15:04:32Z","timestamp":1787756672000},"page":"1008","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic Characterization of Adventitious Root Formation in Cunninghamia lanceolata (Lamb.) Hook. During Cutting Propagation"],"prefix":"10.3390","volume":"17","author":[{"given":"Yuting","family":"Wei","sequence":"first","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China"},{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyi","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China"},{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zezhong","family":"Lin","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liming","family":"Zhu","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8466-0561","authenticated-orcid":false,"given":"Zhaodong","family":"Hao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shunde","family":"Su","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuijin","family":"Luo","sequence":"additional","affiliation":[{"name":"Jiangle State-Owned Forest Farm of Fujian Province, Sanming 353300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoli","family":"Jiang","sequence":"additional","affiliation":[{"name":"Jiangle State-Owned Forest Farm of Fujian Province, Sanming 353300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Ye","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingfeng","family":"Yu","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinhui","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renhua","family":"Zheng","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Forest Cultivation and Forest Products Processing and Utilization, Fujian Academy of Forestry Sciences, Fuzhou 350012, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"122868","DOI":"10.1016\/j.indcrop.2026.122868","article-title":"Multi-trait evaluation and selection of elite Cunninghamia lanceolata provenances for high-quality, large-diameter and knot-free timber","volume":"241","author":"Chen","year":"2026","journal-title":"Ind. Crops Prod."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"7279","DOI":"10.1038\/s41467-026-73756-z","article-title":"Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding","volume":"17","author":"Hao","year":"2026","journal-title":"Nat. Commun."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"13814","DOI":"10.1038\/s41598-017-13219-0","article-title":"Genetic Characterization of Chinese fir from Six Provinces in Southern China and Construction of a Core Collection","volume":"7","author":"Duan","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"113656","DOI":"10.1016\/j.indcrop.2021.113656","article-title":"Comparative metabolomics analysis reveals the color variation between heartwood and sapwood of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook","volume":"169","author":"Yang","year":"2021","journal-title":"Ind. Crops Prod."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Li, L., Deng, X., Zhang, T., Tian, Y., Ma, X., and Wu, P. (2022). Propagation Methods Decide Root Architecture of Chinese Fir: Evidence from Tissue Culturing, Rooted Cutting and Seed Germination. Plants, 11.","DOI":"10.3390\/plants11192472"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1007\/s10265-024-01602-8","article-title":"Hormone functions in adventitious root formation during cutting propagation of woody plants","volume":"138","author":"Liu","year":"2025","journal-title":"J. Plant Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"100385","DOI":"10.1016\/j.cpb.2024.100385","article-title":"Auxin signaling, transport, and regulation during adventitious root formation","volume":"40","author":"Adem","year":"2024","journal-title":"Curr. Plant Biol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Zhou, J.-J., and Luo, J. (2018). The PIN-FORMED Auxin Efflux Carriers in Plants. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19092759"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41438-020-00364-3","article-title":"Auxin regulation and MdPIN expression during adventitious root initiation in apple cuttings","volume":"7","author":"Guan","year":"2020","journal-title":"Hortic. Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1111\/nph.70696","article-title":"OsSEC3A, a key exocyst subunit, is required for the emergence of crown root in rice","volume":"249","author":"Zhu","year":"2026","journal-title":"New Phytol."},{"key":"ref_11","first-page":"38","article-title":"Rooting Mechanism of Rooted Cutting of Cunninghamia lanceolata Clone","volume":"11","author":"He","year":"1994","journal-title":"J. Zhejiang A&F Univ."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"5046","DOI":"10.1038\/s41598-017-05295-z","article-title":"Optimization of hormone combinations for root growth and bud germination in Chinese fir (Cunninghamia lanceolata) clone leaf cuttings","volume":"7","author":"Li","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_14","first-page":"139","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Biogeosciences"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS A J. Integr. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"D265","DOI":"10.1093\/nar\/gkz991","article-title":"CDD\/SPARCLE: The conserved domain database in 2020","volume":"48","author":"Shennan","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Gabaldon","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Misener, S., and Krawetz, S.A. (1999). Primer3 on the WWW for General Users and for Biologist Programmers. Bioinformatics Methods and Protocols, Humana Press.","DOI":"10.1385\/1592591922"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1111\/tpj.16077","article-title":"The plant peptide hormone phytosulfokine promotes somatic embryogenesis by maintaining redox homeostasis in Cunninghamia lanceolata","volume":"113","author":"Hao","year":"2022","journal-title":"Plant J."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2\u2212\u0394\u0394CT Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2238","DOI":"10.1111\/tpj.17087","article-title":"A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce","volume":"120","author":"Canovi","year":"2024","journal-title":"Plant J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1007\/s11033-025-10578-0","article-title":"Comparative analysis of rooting abilities between cuttings of trifoliate orange and Micro-Tom tomato: Hormonal and molecular insights into adventitious root formation","volume":"52","author":"Gobena","year":"2025","journal-title":"Mol. Biol. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4698","DOI":"10.1038\/s41598-020-61611-0","article-title":"Genome survey of Chinese fir (Cunninghamia lanceolata): Identification of genomic SSRs and demonstration of their utility in genetic diversity analysis","volume":"10","author":"Lin","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Lin, S.-Z., Chen, Y., Wu, C., Sun, W.-H., Li, Z., Chen, H., Wang, J., Ji, C., Li, S.-B., and Wang, Z. (2022). Chinese fir genome and the evolution of gymnosperms. bioRxiv.","DOI":"10.1101\/2022.10.25.513437"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Zhang, F., Ren, J., and Wang, C. (2025). Multi-omics analysis reveals the mechanism of adventitious roots formation in peach green branch cuttings. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1740503"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Xiong, Y., Chen, X., Liu, J., Li, Y., Bian, Z., Zhang, X., Zeng, S., da Silva, J.A.T., and Ma, G. (2024). Comparative transcriptomic and hormonal analyses reveal potential regulation networks of adventitious root formation in Metasequoia glyptostroboides Hu et Cheng. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10989-6"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Ahkami, A., Scholz, U., Steuernagel, B., Strickert, M., Haensch, K.-T., Druege, U., Reinhardt, D., Nouri, E., von Wir\u00e9n, N., and Franken, P. (2014). Comprehensive Transcriptome Analysis Unravels the Existence of Crucial Genes Regulating Primary Metabolism during Adventitious Root Formation in Petunia hybrida. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0100997"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1093\/pcp\/pcs035","article-title":"The Interaction and Integration of Auxin Signaling Components","volume":"53","author":"Hayashi","year":"2012","journal-title":"Plant Cell Physiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"110363","DOI":"10.1016\/j.isci.2024.110363","article-title":"Indole-3-propionic acid regulates lateral root development by targeting auxin signaling in Arabidopsis","volume":"27","author":"Sun","year":"2024","journal-title":"iScience"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Liu, X., Zhang, Y., Dai, X., Wang, J., Zheng, Y., and Zhang, T. (2026). Mechanistic insights into adventitious root formation in Cinnamomum kanehirae stem cuttings based on phenotypic, physiological, and transcriptomic analyses. BMC Plant Biol., 26.","DOI":"10.1186\/s12870-026-08827-w"},{"key":"ref_36","first-page":"104","article-title":"Effects of Rooting Powder Treatment on Rooting and Endogenous Hormone Contents in Cunninghamia lanceolata Cuttings","volume":"47","author":"Zhu","year":"2019","journal-title":"Jiangsu Agric. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1111\/j.1399-3054.1990.tb05675.x","article-title":"Ethylene accelerates the breakdown of cytokinins and thereby stimulates rooting in Norway spruce hypocotyl cuttings","volume":"80","author":"Bollmark","year":"1990","journal-title":"Physiol. Plant."},{"key":"ref_38","first-page":"13","article-title":"Research Progress on the Hormonal Regulation Related to Adventitious Root Regeneration and Cuttings Rooting in Plants","volume":"46","author":"Wu","year":"2026","journal-title":"Bull. Bot. Res."},{"key":"ref_39","first-page":"133","article-title":"Relationship Between Adventitious Root Formation and Plant Hormones","volume":"41","author":"Jinxiang","year":"2005","journal-title":"Plant Physiol. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Velada, I., Cardoso, H., Porfirio, S., and Peixe, A. (2020). Expression Profile of PIN-Formed Auxin Efflux Carrier Genes during IBA-Induced In Vitro Adventitious Rooting in Olea europaea L.. Plants, 9.","DOI":"10.3390\/plants9020185"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1008\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T15:09:28Z","timestamp":1787756968000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1008"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,26]]},"references-count":40,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["genes17091008"],"URL":"https:\/\/doi.org\/10.3390\/genes17091008","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,26]]}}}