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 ).

Walnut ( Juglans ) species are used as nut crops worldwide. Eastern black walnut (EBW, Juglans nigra ), a diploid, horticultural important woody species is native to much of eastern North America . Although it is highly valued for its wood and nut, there are few resources for understanding EBW genetics. Here, we present a high-quality genome assembly of J. nigra based on Illumina, Pacbio, and Hi-C technologies. The genome size was 540.8 Mb, with a scaffold N50 size of 35.1 Mb, and 99.0% of the assembly was anchored to 16 chromosomes. Using this genome as a reference, the resequencing of 74 accessions revealed the effective population size of J. nigra declined during the glacial maximum. A single whole-genome duplication event was identified in the J. nigra genome. Large syntenic blocks among J. nigra , Juglans regia , and Juglans microcarpa predominated, but inversions of more than 600 kb were identified. By comparing the EBW genome with those of J. regia and J. microcarpa , we detected InDel sizes of 34.9 Mb in J. regia and 18.3 Mb in J. microcarpa , respectively. Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR ( NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT ) genes were upregulated during the development of walnut husks and shells compared to developing embryos. We also identified candidate genes with essential roles in seed oil synthesis, including FAD ( FATTY ACID DESATURASE ) and OLE ( OLEOSIN ). Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops, and also provides an essential resource for conducting genomics-enabled breeding in walnut.