Journal Article

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

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

2025

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Alcohol / Analysis / Animal Genetics and Genomics / Biomedical and Life Sciences / Chromosome 1 / Chromosomes / Clustering / Cultivars / Diseases and pests / Domestication / Environmental aspects / Ethanol / Food industry / Fruits / Genetic aspects / Genetic structure / Genetic Variation / Genome assembly / Genome, Plant / Genomes / Genotype & phenotype / Growth / Heterozygosity / Hi-C / Interspecific hybridization / Leaves / Life Sciences / Lythraceae - genetics / Microarrays / Microbial Genetics and Genomics / Nucleotides / Phenols / Phylogeny / Plant Genetics and Genomics / Pomegranate / Pomegranate - classification / Pomegranate - genetics / Pomegranates / Positive selection / Proteomics / Punica granatum / Seedlings / Trees