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).