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 (<i>Juglans nigra</i>)

Abstract

Walnut (<i>Juglans</i>) species are used as nut crops worldwide. Eastern black walnut (EBW, <i>Juglans nigra</i>), a diploid, horticultural important woody species is native to much of eastern North America<i>.</i> 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 <i>J. nigra</i> 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 <i>J. nigra</i> declined during the glacial maximum. A single whole-genome duplication event was identified in the <i>J. nigra</i> genome. Large syntenic blocks among <i>J. nigra</i>, <i>Juglans regia</i>, and <i>Juglans microcarpa</i> predominated, but inversions of more than 600 kb were identified. By comparing the EBW genome with those of <i>J. regia</i> and <i>J. microcarpa</i>, we detected InDel sizes of 34.9 Mb in <i>J. regia</i> and 18.3 Mb in <i>J. microcarpa</i>, respectively. Transcriptomic analysis of differentially expressed genes identified five presumed <i>NBS-LRR</i> (<i>NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT</i>) 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 <i>FAD</i> (<i>FATTY ACID DESATURASE</i>) and <i>OLE</i> (<i>OLEOSIN</i>). 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.