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Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears

文献类型： 外文期刊

作者： Sun, Manyi 1 ; Cao, Beibei 1 ; Li, Kui 3 ; Li, Jiaming 1 ; Liu, Jun 4 ; Xue, Cheng 5 ; Gu, Kaidi 5 ; Xu, Shaozhuo 1 ; Li, Yuanjun 6 ; Li, Qingyu 6 ; Qu, Meina 6 ; Zhang, Mingyue 5 ; Wang, Runze 1 ; Liu, Yueyuan 1 ; Yao, Chenjie 1 ; He, Hang 3 ; Wu, Jun 1 ;

作者机构： 1.Nanjing Agr Univ, Coll Hort, State Key Lab Crop Genet & Germplasm Enhancement &, Nanjing, Peoples R China

2.Zhongshan Biol Breeding Lab, Nanjing, Peoples R China

3.Peking Univ, Inst Adv Agr Sci, Natl Key Lab Wheat Improvement, Shandong Lab Adv Agr Sci Weifang, Weifang, Peoples R China

4.Beijing Acad Agr & Forestry Sci, Inst Forestry & Pomol, Beijing, Peoples R China

5.Shandong Agr Univ, Coll Hort Sci & Engn, State Key Lab Crop Biol, Tai An, Peoples R China

6.Yantai Acad Agr Sci, Yantai, Peoples R China

7.Anhui Agr Univ, Sch Hort, Hefei, Peoples R China

期刊名称：NATURE GENETICS （ 影响因子：29.0； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2025 年 57 卷 8 期

页码：

收录情况： SCI

摘要： Pears (Pyrus spp.) are self-incompatible crops with broad genetic diversity. High heterozygosity and technical limitations result in gaps within reference genomes. Our study presents the telomere-to-telomere, haplotype-resolved genomes of a representative Asian pear 'Dangshansuli' (Pyrus bretschneideri) and a European pear 'Max Red Bartlett' (Pyrus communis). Haplotype-specific genes exhibited notable differences from biallelic genes regarding transposable content, methylation patterns and expression levels. Allele-specific expression analysis suggested that the dominance effect is vital in the formation of fruit quality of pears. Population analysis of 362 accessions revealed that interspecific introgression increased pear diversity. We constructed a graph-based genome and identified structural variations associated with agronomic traits. A 286-bp insertion in the promoter region, along with differential expression of PyACS1, was identified between Asian and European pears, which exhibit distinct fruit-softening characteristics. Further experiments demonstrated the role of PyACS1 in fruit softening. Overall, this study provided insights into genetic variation and will facilitate pear improvement.

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