From Genome to Gene Expression: The Genomic Landscape of a Hybrid Species of Eucalyptus urophylla × Eucalyptus grandis and Its Divergence from Parental Species Hybrid

Background Eucalyptus urophylla × Eucalyptus grandis ( E. urograndis ) is a globally significant forest tree species renowned for its rapid growth, high yield, and exceptional wood production efficiency. A comparative analysis of its parental genomes, coupled with an in-depth investigation of the expression patterns of wood-related genes, will provide critical genomic resources to enhance research and utilization of this superior hybrid eucalyptus species. Results In this study, we present a draft genome assembly consisting of 592.09 Mb of data, with 99.91% anchored to 11 pseudochromosomes. The assembly achieved a contig N50 of up to 3.73 Mb and a scaffold N50 of up to 58.62 Mb. Gene annotation and evaluation revealed that the E. urograndis genome contains 32,151 genes, of which 93.5% were fully annotated using Benchmarking Universal Single-Copy Orthologs (BUSCOs). Based on evolutionary analysis, E. grandis and E. urograndis are estimated to have diverged approximately 2.9 million years ago (Mya). Additionally, 131 gene families were found to be significantly expanded, and 475 positively selected genes (PSGs) were identified in the E. urograndis genome. Furthermore, RNA sequencing (RNA-seq) technology was employed to analyze allele-specific expression patterns of key enzymes involved in cellulose, xylan, and lignin biosynthesis. Several allele-specific expression genes (ASEGs) were identified, potentially associated with heterosis in E. urograndis . Conclusions The chromosomal-level genome assembly of E. urograndis presented in this study serves as a valuable genomic resource for eucalyptus molecular breeding, provides novel insights into its evolution, wood formation improvement, and adaptability, and enhances our understanding of the genetic and molecular mechanisms underlying heterosis in Eucalyptus hybrids.