Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits

文献类型： 外文期刊

第一作者： Lu, Xue-Mei

作者： Lu, Xue-Mei;Yu, Xiao-Fen;Qu, Ming-Hao;Man, Yu-Ping;Jiang, Xiao-Han;Li, Mu-Zi;Wang, Jian;Chen, Qi-Qi;Lei, Rui;Zhao, Cheng-Cheng;Zhou, Yun-Qiu;Jiang, Zheng-Wang;Li, Zuo-Zhou;Li, Jie-Wei;Mo, Quan-Hui;Zhang, Ying;Lou, Xin;Peng, Hai-Xu;Yi, Ya-Ting;Wang, He-Xin;Zhang, Xiu-Jun;Li, Li;Zhang, Qiong;Gao, Lei;Wang, Yan-Chang;Li, Guo-Qiang;Lou, Xin;Wang, He-Xin;Wang, Yi-Bo;Qu, Ming-Hao;Jiang, Xiao-Han;Li, Mu-Zi;Zhou, Yun-Qiu;Peng, Hai-Xu;Yi, Ya-Ting;Wang, Huan;Zheng, Shang;Liu, Chuang;Dong, Chang;Wang, Bai-Lin;Sun, Yan-Xiang;Zhang, Hui-Qin;Li, Jie-Wei;Mo, Quan-Hui;Zhang, Ying;Lou, Xin;Wang, He-Xin;Peng, Hai-Xu;Yi, Ya-Ting;Wang, Dan;Wang, Wen-Xia;Liu, Yongbo;Gao, Lei;Wu, Jin-Hu

作者机构：

关键词： kiwiberry; dioecism; adaptive evolution; paleoclimate; GEA; rapid softening

期刊名称：PLANT COMMUNICATIONS （ 影响因子：9.4； 五年影响因子：9.4 ）

ISSN： 2590-3462

年卷期： 2024 年 5 卷 6 期

页码：

收录情况： SCI

摘要： Actinidia arguta , the most widely distributed Actinidia species and the second cultivated species in the genus, can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit, rapid softening, and excellent cold tolerance. Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear. Here, we generated a chromosome -scale genome assembly of an autotetraploid male A. arguta accession. The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo -chromosomes. Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups, Southern and Northern, which first diverged 12.9 million years ago. A. arguta underwent two prominent expansions and one demographic bottleneck from the midPleistocene climate transition to the late Pleistocene. Population genomics studies using paleoclimate data enabled us to discern the evolution of the species' adaptation to different historical environments. Three genes ( AaCEL1 , AaPME1 , and AaDOF1 ) related to flesh softening were identified by multi-omics analysis, and their ability to accelerate flesh softening was verified through transient expression assays. A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome (Chr3) or autosomal chromosomes showed biased expression during stamen or carpel development. This chromosome -level assembly of the autotetraploid A. arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A. arguta .

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