{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T14:47:19Z","timestamp":1787582839869,"version":"build-2736575974"},"reference-count":92,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2022,12,10]],"date-time":"2022-12-10T00:00:00Z","timestamp":1670630400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China","award":["31770650"],"award-info":[{"award-number":["31770650"]}]},{"name":"National Natural Science Foundation of China","award":["2019QZKK0404"],"award-info":[{"award-number":["2019QZKK0404"]}]},{"name":"Second Tibetan Plateau Scientific Expedition and Research Program","award":["31770650"],"award-info":[{"award-number":["31770650"]}]},{"name":"Second Tibetan Plateau Scientific Expedition and Research Program","award":["2019QZKK0404"],"award-info":[{"award-number":["2019QZKK0404"]}]},{"name":"Fundamental Research Funds for the Central Universities","award":["31770650"],"award-info":[{"award-number":["31770650"]}]},{"name":"Fundamental Research Funds for the Central Universities","award":["2019QZKK0404"],"award-info":[{"award-number":["2019QZKK0404"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>The fast-growing arbor poplar is widely distributed across the world and is susceptible to nitrogen availability. The WRKY transcription factor is an important regulatory node of stress tolerance as well as nutrient utilization. However, the potential response mechanism of WRKY genes toward nitrogen is poorly understood. Therefore, the identification of WRKY genes on the Populus trichocarpa genome was performed, and 98 PtWRKYs (i.e., PtWRKY1 to PtWRKY98) were identified. Phylogenetic analysis and the promoter cis-acting element detection revealed that PtWRKYs have multiple functions, including phosphorus and nitrogen homeostasis. By constructing multilayer-hierarchical gene regulatory networks (ML-hGRNs), it was predicted that many WRKY transcription factors were involved in the nitrogen response, such as PtWRKY33 and PtWRKY95. They mainly regulated the expression of primary nitrogen-responsive genes (NRGs), such as PtNRT2.5A, PtNR2 and PtGLT2. The integrative analysis of transcriptome and RT-qPCR results show that the expression levels of 6 and 15 PtWRKYs were regulated by nitrogen availability in roots and leaves, respectively, and those were also found in ML-hGRN. Our study demonstrates that PtWRKYs respond to nitrogen by regulating NRGs, which enriches the nitrate-responsive transcription factor network and helps to uncover the hub of nitrate and its related signaling regulation.<\/jats:p>","DOI":"10.3390\/genes13122324","type":"journal-article","created":{"date-parts":[[2022,12,12]],"date-time":"2022-12-12T03:02:37Z","timestamp":1670814157000},"page":"2324","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Genome-Wide Identification of WRKY Family Genes and the Expression Profiles in Response to Nitrogen Deficiency in Poplar"],"prefix":"10.3390","volume":"13","author":[{"given":"Yao","family":"Chen","sequence":"first","affiliation":[{"name":"Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangge","family":"Kong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le","family":"Yang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7670-9492","authenticated-orcid":false,"given":"Mingyue","family":"Fu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5322-9704","authenticated-orcid":false,"given":"Sheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1007\/s00299-021-02691-8","article-title":"WRKY transcription factors and plant defense responses: Latest discoveries and future prospects","volume":"40","author":"Wani","year":"2021","journal-title":"Plant Cell Rep."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1104\/pp.19.00685","article-title":"WRKY1 mediates transcriptional crosstalk between light and nitrogen signaling pathways in Arabidopsis thaliana","volume":"181","author":"Heerah","year":"2019","journal-title":"Plant Physiol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Singh, A., Sharma, A.K., Singh, N.K., Sonah, H., Deshmukh, R., and Sharma, T.R. 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