Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

文献类型： 外文期刊

第一作者： Sun, Xuepeng

作者： Sun, Xuepeng;Jiao, Chen;Fei, Zhangjun;Schwaninger, Heidi;Chao, C. Thomas;Zhong, Gan-Yuan;Ma, Yumin;Duan, Naibin;Khan, Awais;Ban, Seunghyun;Xu, Kenong;Cheng, Lailiang;Fei, Zhangjun

作者机构：

期刊名称：NATURE GENETICS （ 影响因子：38.33； 五年影响因子：36.431 ）

ISSN： 1061-4036

年卷期： 2020 年 52 卷 12 期

页码：

收录情况： SCI

摘要： Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies similar to 23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel similar to 19% of genes displaying allele-specific expression, including many associated with fruit quality.

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