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Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication

文献类型： 外文期刊

作者： Su, Ying 1 ; Yang, Xuanwen 2 ; Wang, Yuwei 1 ; Li, Jialei 1 ; Long, Qiming 2 ; Cao, Shuo 2 ; Wang, Xu 2 ; Liu, Zhenya 2 ; Huang, Siyang 2 ; Chen, Zhuyifu 2 ; Peng, Yanling 2 ; Zhang, Fan 2 ; Xue, Hui 2 ; Cao, Xuejing 2 ; Zhang, Mengyan 2 ; Yisilam, Gulbar 1 ; Chu, Zhenzhou 1 ; Gao, Yuan 4 ; Zhou, Yongfeng 2 ; Liu, Zhongjie 2 ; Xiao, Hua 2 ; Tian, Xinmin 1 ;

作者机构： 1.Xinjiang Univ, Coll Life Sci & Technol, Xinjiang Key Lab Biol Resources & Genet Engn, Urumqi 830046, Xinjiang, Peoples R China

2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr & Rural Affairs, Natl Key Lab Trop Crop Breeding,Shenzhen Branch,Gu, Shenzhen 518120, Peoples R China

3.Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Natl Key Lab Germplasm Innovat & Utilizat Hort Cro, Zhengzhou 450009, Peoples R China

4.Chinese Acad Agr Sci, Res Inst Pomol, Key Lab Hort Crop Germplasm Resources Utilizat, Minist Agr & Rural Affairs Peoples Republ China, Xingcheng 125100, Peoples R China

5.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Natl Key Lab Trop Crop Breeding, Haikou 571101, Peoples R China

6.Guangxi Normal Univ, Key Lab Ecol Rare & Endangered Species & Environm, Minist Educ, Guilin 541006, Peoples R China

7.Guangxi Normal Univ, Guangxi Key Lab Landscape Resources Conservat & Su, Guilin 541006, Peoples R China

期刊名称：PLANT PHYSIOLOGY （ 影响因子：7.4； 五年影响因子：8.7 ）

ISSN： 0032-0889

年卷期： 2024 年

页码：

收录情况： SCI

摘要： The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies and breeding programs. In this study, we assembled a haplotype-resolved telomere-to-telomere (T2T) reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on 12 assemblies from wild and cultivated species to investigate the dynamic changes of functional genes. Our results revealed the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Our analyses also demonstrated a higher prevalence of different types of resistance gene analogs (RGAs) in cultivars than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR, NB-ARC-LRR, and CC-NB-ARC-LRR genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding. A haplotype-resolved T2T reference genome for apple and pan-genomic analyses of wild and cultivated apple species elucidates the mechanisms of the dynamic expansion resistance genes during apple domestication.

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