De novo chromosome-level genome assembly of Chinese walnut (Juglans cathayensis Dode)

Abstract

Chinese walnut (Juglans cathayensis Dode), is a diploid, woody species native to China. It has 16 chromosomes (2n =2x= 32), as do all members of its genus and most members of its family (Juglandaceae). Although high-quality sequence data and reference genomes are available for several Juglans species, our goal was to produce a de novo, chromosome-level assembly of the Chinese walnut genome to gain insights into the species' evolution and biology. Our assembly was based on Nanopore long reads and chromosome conformation capture (Hi-C) data. The final assembly showed a contig N50 size of 6.49 Mb and a scaffold N50 size of 36.1 Mb. The final genome size of Chinese walnut was estimated to be 548 Mb. The sixteen scaffolds of the assembly anchored 99 % of the Chinese walnut genome. The assembly of the gene space (BUSCO) was 92.0 %. We annotated 29,032 protein coding genes with a mean of 6 exons per gene. We detected 2,993 non-coding RNA in the genome. A phylogenetic analysis based on 552 single-copy orthologs indicated that Chinese walnut close relative to Persian walnut (J. regia). The collinearity analysis showed that two whole genome duplication (WGD) events in J. cathayensis and J. regia from a common ancestor. Comparative genome analysis of J. cathayensis versus J. regia showed that 399 and 1,528 gene families were expanded and contracted respectively in the Chinese walnut genome. This J. cathayensis genome should be a useful resource for study of the evolution, breeding, and genetic variation in walnuts (Juglans).