The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

Abstract

Background Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value. Findings Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 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%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics 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 CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified. Conclusions Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.

Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

“…Genome-wide data of J. mandshurica were downloaded from NGDC ( , PRJCA006358 (accessed on 8 October 2021)) [ 54 ]. The Markov (HMM) profile of the AP2 domain (PF00847) was obtained from the Pfam database ( (accessed on 8 October 2021)).…”

Integrated metabolomic and transcriptomic analyses reveal different metabolite biosynthesis profiles of Juglans mandshurica in shade

“…The two shading treatments with the highest seedling height and the control were selected according to seedling height to investigate the changes in gene expression levels. The J. mandshurica genome was used as the reference genome ( Li et al, 2022 ). Three samples (N, L50 and L20) were used to construct nine cDNA libraries.…”

Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

“…In some cases, a single NBS-LRR gene of J. nigra showed high similarity and collinearity with an entire cluster of NBS-LRR genes of J. regia . The expansion and clustering of genes related to resistance has also been observed in the WAK ( WALL ASSOCIATED KINASE WAK/WAKL ) gene family in Persian walnut and J. mandshurica [ 52 ], and it is believed to be related to maintenance of key functions, neo-functionalization, and in some cases, as in the species-specific duplication and clusters of NBS-LRR , evolution in response to selection pressure [ 52–54 ].…”

“…The oil content of most Juglans species is poorly characterized, presenting an opportunity for comparative metabolomics to contribute to our understanding of seed oil production [ 52 , 63 ]. Seed oil content and composition have not (yet) been important targets for improvement in J. nigra , although they are in other oil seed crops, including J. regia [ 63 ].…”