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)

Abstract

Walnut (Juglans) species are used as nut crops worldwide. Eastern black walnut (EBW, J. 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, J. regia, and J. 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.

Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea)

“…WAK are increasingly associated with plant immunity, including neo- and sub-functionalization in response to changing selection pressure ( Stephens et al . 2022 ; Zhou et al . 2023 ).…”

“…A macrosynteny analysis was conducted using MCscan (Python version) and jcvi (v.1.3.3) with available Juglans species, including J. cinerea (PRJEB56451), J. nigra ( Zhou et al . 2023 ), J. regia (PRJNA291087), and J. mandshurica (PRJCA006358) ( Tang et al .…”

Chromosome-level genome assembly of Platycarya strobilacea

“…Genome annotation was predicted using multiple methods, including transcriptomic data, de novo prediction, and homology-based annotation methods 19 . The details of genome annotation follow the pipeline are shown in Fig.…”

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

“…To further understand the important genes CBF1 and ICE1 genes in angiosperms, we used the one-to-one ortholog method to identify the two genes in a total of nineteen plant genomes ( J. regia , ‘Chandler’; J. regia , ‘Zhongmucha-1’; J. sigillata , J. nigra , J. microcarpa , J. mandshurica , Carya cathayensis , Castanea mollissima , Quercus robur , Sesamum indicum , Malus pumila , Populus trichocarpa , Vitis vinifera , Olea europaea , Arabidopsis thaliana , Theobroma cacao , Oryza sativa , Zea mays , and Triticum aestivum ,) ( Table S1 ) [ 20 , 23 , 43 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 ]. We analyzed the phylogenetic relationships, conserved domains, gene structures, and motifs of all CBF and ICE proteins [ 88 , 95 ].…”