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Background <p>The pomegranate is cultivated across a wide range of geographical regions worldwide for ornamental purposes, fruit aril for the food industry, and juice production. The pomegranate genome is reported to consist of 2n = 16 chromosomes in some cultivars and 2n = 18 in others. Clustering assembled contigs using Hi-C technology resulted in eight pseudochromosomes, alternatively, anchoring these contigs onto a genetic map produced nine pseudochromosomes. The origin of the domesticated pomegranate is unknown. Previous studies have suggested that the variant Daru, which is grown in the region of India and Nepal, is the origin of the wild stock.</p> Results <p>Here we explored the phylogeny, genetic structure, and substitution pattern of <i>P. granatum</i>. Phylogenetic analysis of <i>Punica granatum</i> accessions revealed that Daru seedlings constitute a distinct clade, which is a sister to the clade of Asian accessions, rather than an outgroup. No evidence of introgression was observed between Daru and cultivated accessions. Analysis of the non-synonymous to synonymous substitutions ratio in genic regions outlines a similar profile of the Daru and the domesticated pomegranates with overall positive selection, while the wild type <i>P. protopunica</i> illustrated a different profile with positive selection only in some regions. Domesticated pomegranate variants show low heterozygosity and nucleotide diversity, particularly on chromosome 1.</p> Conclusions <p>Our findings suggest that differences in chromosome numbers may be associated with the formation of chromosome quadrivalents and their impact on the arrangement of contigs into pseudochromosomes. The profile of Kn to Ks ratio in domesticated pomegranates likely reflects positive selection. Genetic profiling of Daru, domesticated <i>P. granatum</i>, and wild-type <i>P. protopunica</i> revealed that Daru more closely resembles domesticated plants, challenging the notion that it represents the wild pomegranate.</p>

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The pomegranate (Punica granatum L. cv. ‘Wonderful’) genome and P. protopunica shed light on pomegranate domestication. Is Daru a wild stock?

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  • 发表日期：

    2025年10月17日

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  • Alexandra Slonimsky,
  • Oleg Lovky,
  • Rotem Harel-Beja,
  • Irit Bar-Ya’akov,
  • Ravit Eshed,
  • Amir Sherman,
  • Doron Holland,
  • Ron Ophir

摘要

Background

The pomegranate is cultivated across a wide range of geographical regions worldwide for ornamental purposes, fruit aril for the food industry, and juice production. The pomegranate genome is reported to consist of 2n = 16 chromosomes in some cultivars and 2n = 18 in others. Clustering assembled contigs using Hi-C technology resulted in eight pseudochromosomes, alternatively, anchoring these contigs onto a genetic map produced nine pseudochromosomes. The origin of the domesticated pomegranate is unknown. Previous studies have suggested that the variant Daru, which is grown in the region of India and Nepal, is the origin of the wild stock.

Results

Here we explored the phylogeny, genetic structure, and substitution pattern of P. granatum. Phylogenetic analysis of Punica granatum accessions revealed that Daru seedlings constitute a distinct clade, which is a sister to the clade of Asian accessions, rather than an outgroup. No evidence of introgression was observed between Daru and cultivated accessions. Analysis of the non-synonymous to synonymous substitutions ratio in genic regions outlines a similar profile of the Daru and the domesticated pomegranates with overall positive selection, while the wild type P. protopunica illustrated a different profile with positive selection only in some regions. Domesticated pomegranate variants show low heterozygosity and nucleotide diversity, particularly on chromosome 1.

Conclusions

Our findings suggest that differences in chromosome numbers may be associated with the formation of chromosome quadrivalents and their impact on the arrangement of contigs into pseudochromosomes. The profile of Kn to Ks ratio in domesticated pomegranates likely reflects positive selection. Genetic profiling of Daru, domesticated P. granatum, and wild-type P. protopunica revealed that Daru more closely resembles domesticated plants, challenging the notion that it represents the wild pomegranate.