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

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-related genes have been associated with genes identified in previous studies, potentially contributing to lignin biosynthesis through these variations and meriting further investigation. This study integrates genome annotation, comparative genomics, and transcriptomics, laying a foundation for functional analysis and molecular breeding for important characteristics of E. cloeziana and thus promoting the cultivation of new varieties of fast-growing trees. • E. cloeziana genome annotation gained completeness and non-coding RNA features. • Comparative genomics reveals gene family expansion in E. cloeziana for wood formation. • Tissue-specific transcriptomic atlas reveals xylem-enriched lignin synthesis genes.