Genome annotation, comparative genomics and transcriptomic analysis of Eucalyptus cloeziana reveal insights into genome evolution and wood formation in Eucalyptus

作者：Meng Li, Weilin Wu, Yi Mo, Xian-Chen Geng, Yuchong Fei, Jiajing Xu, Deyuan Lei, Yanqi Cen, Jun Ni, Kuipeng Li, Yunpeng Cao, Zeng‐Fu Xu · 发表于：Industrial Crops and Products · 年份：2025 · DOI：10.1016/j.indcrop.2025.121680 · 被引用次数：3 · 研究领域：Plant Pathogens and Fungal Diseases、Plant and Fungal Interactions Research、Phytoplasmas and Hemiptera pathogens

Eucalyptus, a fast-growing tree species, has significant economic and ecological value. Eucalyptus cloeziana , known for its excellent wood properties, is extensively used to produce high-end furniture, highlighting its economic importance. However, the existing genome annotations and gene expression data for E. cloeziana are still insufficient for its molecular genetic improvement. Based on the E. cloeziana genome assembly data from the NCBI-GenBank, this study systematically annotated its whole genome. Our genome annotation improved the BUSCO completeness score by nearly 10 %, identifying 41,610 genes and 2089 non-coding RNAs. Through comparative transcriptomic analysis across tissues, we characterized the tissue-specific gene expression patterns in E. cloeziana , and found that xylem-specific genes were highly enriched in the lignin biosynthesis-related pathway. Molecular evolutionary analyses revealed that E. cloeziana and E. grandis underwent whole-genome duplication, indicating the evolution of Eucalyptus species. Gene family analysis revealed significant expansion in E. cloeziana gene families involved in secondary cell wall and lignin biosynthesis. Key gene families related to lignin synthesis, such as cinnamoyl-CoA reductase , caffeoyl-CoA 3-O-methyltransferase , cinnamate 4-hydroxylase and 4-coumarate: CoA ligase , expanded and were highly expressed in the xylem, which may explain its excellent wood properties. Certain structural variations in lignin biosynthesis-re...