Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar"Qiu Jinxing."We assembled an 823.41 Mb genome encoding 40571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64％ of the assembled ge-nome. Phylogenomic analyses revealed that culti-vated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been sig-nificantly amplified in the hawthorn genome. In ad-dition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the ex-pansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or al-lopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.

Ticao Zhang;Qin Qiao;Xiao Du;Xiao Zhang;Yali Hou;Xin Wei;Chao Sun;Rengang Zhang;Quanzheng Yun;M.James C.Crabbe;Yves Van de Peer;Wenxuan Dong

College of Chinese Material Medica,Yunnan University of Chinese Medicine,Kunming 650500,China;School of Agriculture,Yunnan University,Kunming 650091,China;College of Horticulture,Shenyang Agricultural University,Shenyang 110866,China;Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education,Nanning Normal University,Guangxi,Nanning 530001,China;Beijing Ori-Gene Science and Technology Co.Ltd,Beijing 102206,China;Wolfson College,Oxford University,Oxford,UK;Institute of Biomedical and Environmental Science & Technology,School of Life Sciences,University of Bedfordshire,Park Square,Luton,UK;School of Life Sciences,Shanxi University,Taiyuan 030006,China;Department of Plant Biotechnology and Bioinformatics,Center for Plant Systems Biology,Ghent University,VIB,9052,Ghent,Belgium;Department of Biochemistry,Genetics and Microbiology,University of Pretoria,Pretoria 0028,South Africa;College of Horticulture,Nanjing Agricultural University,Nanjing 210095,China

植物学报（英文版）

[1]Ticao Zhang;Qin Qiao;Xiao Du;Xiao Zhang;Yali Hou;Xin Wei;Chao Sun;Rengang Zhang;Quanzheng Yun;M.James C.Crabbe;Yves Van de Peer;Wenxuan Dong-.Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe))[J].植物学报（英文版）,2022(08):1487-1501

Maleae,Jinxing,tetraploidization,retrotransposons,autopolyploidization,lopolyploidization

Cultivated,hawthorn,Crataegus,pinnatifida,major,sheds,light,evolution,apple,tribe,important,medicinal,edible,plant,long,history,health,protection,China,Herein,novo,level,sequence,cultivar,Qiu,We,assembled,Mb,encoding,genes,further,anchored,into,pseudo,chromosomes,which,account,Phylogenomic,analyses,revealed,that,diverged,from,other,species,within,approximately,Mya,Notably,involved,flavonoid,triterpenoid,biosynthetic,pathways,have,been,sig,nificantly,amplified,In,ad,dition,results,indicated,share,unique,ancient,event,however,recent,independent,whole,duplication,was,specifically,detected,amplification,terminal,repeat,contributed,most,pansion,Furthermore,identified,two,paleo,sub,genomes,extant,found,these,showed,different,rearrangement,mechanisms,also,reconstructed,ancestral,Rosaceae,discussed,possible,origin,patterns,Overall,study,provides,improved,context,understanding,this,new,high,quality,reference,useful,resource,horticultural,improvement

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