A chromosome-scale genome assembly of Acacia melanoxylon provides new insights into its root nodule and heartwood formation

Acacia melanoxylon, commonly known as Blackwood, is a valuable commercial wood and an important ecological tree species owing to its high-quality appearance-grade heartwood products and nitrogen fixation ability. However, the lack of a complete genome sequence has hindered biological research and applied studies, especially in analyzing and exploring genes related in nodule and heartwood formation in Blackwood. Here, we present the first complete genome of the Acacia by combining Illumina, PacBio, BioNano and HiC sequencing technologies. This high-quality assembly encompasses a 680 Mb genome (scaffolds N50 = 6.66 Mb), which mapped onto 13 chromosome with 58.31 % repetitive sequences. Genome evolution analysis revealed that two whole-genome duplication events occurred in A. melanoxylon. The expansion of the WRKY and R (disease- resistance) gene families particularly WRKY47 and WRKY24, is linked to the Blackwood's strong adaptability. Additionally, the PHYB (Phytochrome B) and RR (response regulator) gene families which are critical for root nodulation, showed significant expansion and exhibited notably high expression in roots and root nodules. Moreover, genes involved in the flavonoid biosynthesis and lignin biosynthesis pathway, such as HCT, CCR, CAD, F3'H, and FGT, play crucial roles in heartwood formation in Blackwood. The high-quality genome will aid functional genetic research and accelerate molecular breeding on Acacia species. Furthermore, it provides new insights into the molecular mechanism underlying nodule and heartwood formation in woody plants.