# The telomere-to-telomere haplotype genome provides in-depth insights into the molecular mechanisms of the anthocyanin deficiency phenotype in Prunus mume

## TL;DR

A complete genome of Prunus mume reveals genetic changes linked to the lack of anthocyanin pigmentation in a specific cultivar.

## Contribution

The study presents a gap-free telomere-to-telomere haplotype genome of Prunus mume f. viridicalyx and identifies key genes involved in anthocyanin deficiency.

## Key findings

- The P. mume f. viridicalyx genome is complete and significantly improves on previous genome assemblies.
- Genes related to anthocyanin, glutathione, and carotenoid metabolism are enriched in domestication-related mutations.
- Early codon termination in the PmGSTF2 gene is linked to reduced anthocyanin accumulation in the cultivar.

## Abstract

Prunus mume originated from China and is highly valued for its remarkable combination of ornamental blossoms and high economic value. Previously published P. mume genomes contain unanchored genetic regions and excessive gaps. Here, we report the P. mume f. viridicalyx gap-free telomere-to-telomere (T2T) haplotype genome. The LE_hap1 and LE_hap2 genomes were 229.29 and 228.36 Mb in length, respectively, with an N50 length of the contig between 27.65 and 27.79 Mb and 24,318 and 24,316 protein-coding genes, respectively. The completeness, continuity, and accuracy of the P. mume f. viridicalyx genome was significantly improved over the previous P. mume genomes. The key mutated genes during P. mume f. viridicalyx cultivar domestication were identified by comparative genomic, population evolution, and selective sweep analyses to be significantly enriched in the anthocyanin metabolism process, glutathione metabolism process, and carotenoid biosynthesis. Further analysis revealed that early codon termination of the PmGSTF2 gene, which is the key gene for the characteristic production of P. mume f. viridicalyx, reduced anthocyanin accumulation. We assembled a complete T2T gap-free haplotype P. mume genome, which provides a reference for gene mining and genome evolution of the anthocyanin deficiency phenotype in P. mume.

The online version contains supplementary material available at 10.1186/s43897-025-00186-8.