DISCUSSION
We report the first assembly of a high-quality, chromosome-level genome
for Chinese walnut using a combination of Illumina HiSeq X Ten,
Nonopore, and Hi-C sequencing platforms. Compared to previously
available genome assemblies for this species, the Scaffold N50 value was
improved 163 fold (contig N50 size of J. cathayensis v2.0 was
23,789,296 bp versus 145,095 bp contig N50 size for J.
cathayensis v1.0), and the final calculated genome size is smaller
(580Mb, v1.0 versus 548Mb, v2.0) (Figure1; Table S12). Through Hi-C, a
chromosome-level genome was obtained with a scaffold size of 36Mb (Table
S12) and scaffolds resolved into 16 chromosomes, unlike the previously
available genome (J. cathayensis v1.0; Stevens et al., 2018)
(Table S5, Table S12) (DeMaere & Darling, 2019; Zhang et al., 2020c;
Chen et al., 2020; Choi et al., 2020). We predicted 29,032
protein-coding genes from the generated assembly. The phylogenetic tree
revealed that Chinese walnut and Persian walnut diverged
~4.6 million years ago. This high-quality
chromosome-level genome will be benefit for breeding and genetic
variation discovery in walnut (Juglans ) species.