Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis
文献类型： 外文期刊
作者： Fan, Chunjie 1 ; Lyu, Mingjie 3 ; Zeng, Bingshan 1 ; He, Qiang 3 ; Wang, Xiaoping 1 ; Lu, Meng-Zhu 2 ; Liu, Bobin 5 ; Liu, Jun 3 ; Esteban, Eddi 6 ; Pasha, Asher 6 ; Provart, Nicholas J. 6 ; Wang, Huan 7 ; Zhang, Jin 2 ;
作者机构： 1.Chinese Acad Forestry, Res Inst Trop Forestry, State Key Lab Tree Genet & Breeding, Key Lab State Forestry & Grassland Adm Trop Forest, Guangzhou, Peoples R China
2.Zhejiang A&F Univ, Coll Forestry & Biotechnol, State Key Lab Subtrop Silviculture, Hangzhou 311300, Zhejiang, Peoples R China
3.Chinese Acad Agr Sci, Natl Key Facil Crop Resources & Genet Improvement, Inst Crop Sci, Beijing, Peoples R China
4.Tianjin Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Tianjin, Peoples R China
5.Yancheng Teachers Univ, Jiangsu Synthet Innovat Ctr Coastal Bioagr, Sch Wetlands, Jiangsu Key Lab Bioresources Saline Soils, Yancheng, Peoples R China
6.Univ Toronto, Ctr Anal Genome Evolut & Funct, Dept Cell & Syst Biol, Toronto, ON, Canada
7.Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100081, Peoples R China
关键词： alternative splicing landscape; coexpression network; ePlant; Eucalyptus grandis; expression atlas
期刊名称：PLANT CELL AND ENVIRONMENT （ 影响因子：7.3； 五年影响因子：8.1 ）
ISSN： 0140-7791
年卷期： 2024 年 47 卷 4 期
页码：
收录情况： SCI
摘要： Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser ().
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