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

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Plant Communications 2021年第6期2卷 96-110页

作者： Lihong Xiao Mengjun Yu Ying Zhang Jie Hu Rui Zhang Jianhua Wang Haobing Guo He Zhang Xinyu Guo Tianquan Deng Saibin Lv Xuan Li Jianqin Huang Guangyi Fan State Key Laboratory of Subtropical Silviculture Zhejiang A&F UniversityNo.666 Wusu St.Lin’an DistrictHangzhou 311300China BGI-Qingdao BGI-ShenzhenNo.2 Hengyunshan Rd.Huangdao DistrictQingdao 266555China BGI Genomics BGI-ShenzhenShenzhen 518083China

pecan(Carya illinoinensis)is a tree nut crop of worldwide economic importance that is rich in healthpromoting ***,pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal ***,we report a high-quality,chromosome-scale genome assembly of the controlled-cross pecan cultivar‘Pawnee’constructed by integrating Nanopore sequencing and Hi-C *** and evolutionary analyses reveal two whole-genome duplication(WGD)events and two paleo-subgenomes in pecan and *** estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from *** two paleo-subgenomes differ in size and protein-coding gene *** exhibit uneven ancient gene loss,asymmetrical distribution of transposable elements(especially LTR/Copia and LTR/Gypsy),and expansions in transcription factor families(such as the extreme pecan-specific expansion in the far-red impaired response 1 family),which are likely to reflect the long evolutionary history of species in the Juglandaceae.A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate *** changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scabsusceptible cultivars‘Excell’and‘Pawnee’.These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in *** high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.

关键词： pecan genome assembly paleo-subgenome pecan scab fungal disease population genetics

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