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

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 

机构地区：[1]State Key Laboratory of Subtropical Silviculture,Zhejiang A&F University,No.666 Wusu St.Lin’an District,Hangzhou 311300,China [2]BGI-Qingdao,BGI-Shenzhen,No.2 Hengyunshan Rd.Huangdao District,Qingdao 266555,China [3]BGI Genomics,BGI-Shenzhen,Shenzhen 518083,China

出　　处：《Plant Communications》2021年第6期96-110,共15页植物通讯（英文）

基　　金：This work was supported by grants from the Natural Science Foundation of Zhejiang Province,China(grant no.Z20C160001);the State Key Laboratory of Subtropical Silviculture at Zhejiang A&F University(grant no.ZY20180202);the Research and Development Fund of Zhejiang A&F University(grant no.2018FR002).

摘　　要：Pecan(Carya illinoinensis)is a tree nut crop of worldwide economic importance that is rich in healthpromoting factors.However,pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases.Here,we report a high-quality,chromosome-scale genome assembly of the controlled-cross pecan cultivar‘Pawnee’constructed 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 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 bayberry.The two paleo-subgenomes differ in size and protein-coding gene sets.They 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 genes.Significant 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 pecan.The 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 

分 类 号：Q78[生物学—分子生物学]