Improved de novo chromosome‐level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode

Abstract Manchurian walnut ( Juglans mandshurica Maxim.) is a synonym of J . cathayensis , a diploid, vulnerable, temperate deciduous tree valued for its wood and nut. It is also valued as a rootstock for Juglans regia because of its reported tolerance of lesion nematode. Reference genomes are available for several Juglans species, our goal was to produce a de novo, chromosome‐level assembly of the J . mandshurica genome. Here, we reported an improved assembly of J . mandshurica with a contig N50 size of 6.49 Mb and a scaffold N50 size of 36.1 Mb. The total genome size was 548 Mb encoding 29,032 protein coding genes which were annotated. The collinearity analysis showed that J . mandshurica and J. regia originated from a common ancestor, with both species undergoing two WGD events. A genomic comparison showed that J . mandshurica was missing 1657 genes found in J. regia , and J . mandshurica includes 2827 genes not found in of the J. regia genome. The J . mandshurica contained 1440 unique paralogues that were highly enriched for flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant‐pathogen interaction. Four gene families related to disease resistance notable contraction (rapidly evolving; LEA , WAK , PPR , and PR ) in J . mandshurica compared to eight species. JmaPR10 and JmaPR8 contained three orthologous gene pairs with J. regia that were highly expressed in root bark. JmaPR10 is a strong candidate gene for lesion nematodes resistance in J . mandshurica . The J . mandshurica genome should be a useful resource for study of the evolution, breeding, and genetic variation in walnuts ( Juglans ).