Chromosome-scale assembly reveals the asymmetric paleo-subgenomes evolution and targets for accelerating fungal resistance breeding in nut crop, pecan

Abstract Pecan (Carya illinoinensis) is a tree nut crop of economic importance worldwide, and rich in healthy factors. However, pecan production and nut quality are largely challenged by environmental stresses, such as outbreak of severe fungal diseases. Here we report a high-quality chromosome-scale genome of a controlled-cross pecan cultivar ‘Pawnee’ by integrating Nanopore sequencing and Hi-C technologies. Phylogenetic and evolutionary analyses reveal two whole-genome duplication (WGD) events and two paleo-subgenomes in pecan and walnut. Time dating suggests that the recent WGD event and considerable genome rearrangements in pecan and walnut account for the expanded genome size and chromosome numbers after diverging with bayberry. The two paleo-subgenomes differ in their size and protein-coding gene sets, and exhibit uneven ancient gene loss, asymmetrical distribution of transposable elements (especially LTR/copia and LTR/gypsy) and transcription factor families (such as the pecan-specific extreme expansion in far-red impaired response1 family), likely reflect the long evolution history of species in Juglandaceae. Whole genome scan for re-sequencing data from 86 pecan scab-associated core accessions identifies 47 selected chromosome regions involving in 185 putative candidate genes. Significant changes were detected on expression regulation of candidate genes that functionally related to chitin response pathway under chitin treatment in pecan scab resistant and susceptible cultivars ‘Excell’ and ‘Pawnee’. These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan. The high-quality sequences are valuable resources for pecan breeders and will provide the foundation and example for production and quality improvement of tree nut crops.