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

Ying SuXuanwen YangYuwei WangJialei LiQiming LongShuo CaoXu WangZhenya LiuSiyang HuangZhuyifu ChenYanling PengFan ZhangHui XueXuejing CaoMengyan ZhangGulbar YisilamZhenzhou ChuYuan GaoYongfeng ZhouZhongjie LiuHua XiaoXinmin Tian
Published in: Plant physiology (2024)
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.
Keyphrases
  • genome wide
  • dna methylation
  • genome wide identification
  • copy number
  • genetic diversity
  • gene expression
  • public health
  • transcription factor
  • wastewater treatment
  • single cell
  • case control
  • life cycle