Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization  

作　　者：Xinyi Zhang Yang Chen Lingyun Wang Ye Yuan Mingya Fang Lin Shi Ruisen Lu Hans Peter Comes Yazhen Ma Yuanyuan Chen Guizhou Huang Yongfeng Zhou Zhaisheng Zheng Yingxiong Qiu 

机构地区：[1]Systematic and Evolutionary Botany and Biodiversity Laboratory,College of Life Sciences,Zhejiang University,Hangzhou,310058,Zhejiang,China [2]CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,Wuhan Botanical Garden,Chinese Academy of Sciences,Wuhan,430074,Hubei,China [3]Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation,Jinhua Academy of Agricultural Sciences(Zhejiang Institute of Agricultural Machinery),Jinhua,321000,Zhejiang,China [4]Jiaxing Academy of Agricultural Sciences,Jiaxing,314016,Zhejiang,China [5]Institute of Botany,Jiangsu Province and Chinese Academy of Sciences,Nanjing 210014,Jiangsu,China [6]Department of Environment&Biodiversity,Salzburg University,Salzburg,5020,Austria [7]State Key Laboratory of Tropical Crop Breeding,Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Key Laboratory of Synthetic Biology,Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518124,Guangdong,China

出　　处：《Horticulture Research》2023年第11期168-179,共12页园艺研究（英文）

基　　金：supported by the collaborative program of Chinese Academy of Agricultural Sciences(CAAS)-Jinhua Academy of Agricultural Sciences,funded by Jinhua City of Zhejiang Province,and the Research Grant fromWuhan Botanic Garden(E1559901)。

摘　　要：Water caltrop(Trapa spp.,Lythraceae)is a traditional but currently underutilized non-cereal crop.Here,we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa.natans(4x,AABB),i.e.,diploid T.natans(2x,AA)and Trapa incisa(2x,BB).In conjunction with four published(sub)genomes of Trapa,we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element(TE)library to develop Trapa genomic resources.The pangenome displayed substantial gene-content variationwith dispensable and private gene clusters occupying a large proportion(51.95%)of the total cluster sets in the six(sub)genomes.Genotyping of presence-absence variation(PAVs)identified 40453 PAVs associated with 2570 genes specific to A-or B-lineages,of which 1428were differentially expressed,andwere enriched in organ development process,organic substancemetabolic process and response to stimulus.Comparative genome analyses showed that the allotetraploid T.natans underwent asymmetric subgenome divergence,with the B-subgenome being more dominant than the A-subgenome.Multiple factors,including PAVs,asymmetrical amplification of TEs,homeologous exchanges(HEs),and homeolog expression divergence,together affected genome evolution after polyploidization.Overall,this study sheds lights on the genome architecture and evolution of Trapa,and facilitates its functional genomic studies and breeding program.

关 键 词：DIVERGENCE EVOLUTION STRUCTURAL 

分 类 号：S645.4[农业科学—蔬菜学]