Supporting data for "The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis"

Manchurian walnut (<i>Juglans mandshurica</i> Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). <i>J. mandshurica</i> produces juglone that is a toxic allelopathic agent and has potential utilization value. <br>Here, we present a high-quality chromosome-scale reference genome assembly and annotation for <i>J. mandshurica</i> (n=16) with a contig N50 of 21 Mb by combining PacBio HiFi reads with Hi-C data. The assembled genome has an estimated sequence size of 548 Mb, and consists of 623 scaffolds and 40,453 protein-coding genes. 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. <i>J. mandshurica</i> displays a close sequence relationship with <i>J. cathayensis</i>, with a divergence time of 13.8 million years ago (mya). Combining the high-quality genome, transcriptome and metabolome data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five <i>CYP450</i> genes were found that may contribute to juglone accumulation. Some candidate regulators (e.g. FUS3, ABI3, LEC2 and WRI1 TFs) involved in the regulation of lipid biosynthesis were also identified. <br>Our genomic data provides new insights into the evolution of the walnut genome and creates a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.