Haplotype-resolved and chromosome-level reference genome assembly of Diospyros deyangensis provides insights into the evolution and juvenile growth of persimmon

TL;DR

This study provides a detailed genome assembly for a wild persimmon species, revealing insights into its evolution and early flowering traits.

Contribution

The study presents a high-quality, haplotype-resolved genome assembly for Diospyros deyangensis and identifies a gene linked to early flowering.

Findings

The D. deyangensis genome assembly reveals an additional whole-genome duplication event after the eudicots' ancient hexaploidy.

Genetic differentiation is observed between D. deyangensis and D. kaki, suggesting distinct evolutionary pathways.

The DdELF4 gene is identified as a flowering repressor through overexpression in Arabidopsis.

Abstract

The Diospyros genus , which includes both wild and cultivated species such as Diospyros lotus and Diospyros kaki, represents a diverse genetic pool with significant agricultural value. In this study, we present a high-quality, haplotype-resolved, chromosome-level genome assembly for Diospyros deyangensis (hereinafter referred to as ‘Deyangshi’), an autotetraploid wild species notable for its short juvenile phase, by integrating high-fidelity single-molecule, nanopore sequencing, and high-throughput chromosome conformation capture techniques. The assembled genome size is ~3.01 Gb, anchored onto 60 pseudochromosomes. Comparative genomic analysis revealed that the D. deyangensis genome underwent an additional whole-genome duplication (WGD) event following the eudicots shared ancient hexaploidy event. Resequencing and clustering on 63 samples representing 11 geographically diverse Diospyros accessions revealed significant genetic differentiation between D. deyangensis and D. kaki, as well as between D. kaki and other Diospyros species using population genomic analyses, suggesting that D. kaki followed an independent evolutionary pathway. Additionally, we identified DdELF4 (EARLY FLOWERING 4) from the ‘Deyangshi’ backcross population using bulked segregant RNA sequencing (BSR-seq) with 50 early-flowering and 50 non-early-flowering individuals. Overexpression of DdELF4 in Arabidopsis resulted in delayed flowering and downregulation of FT gene expression, indicating its role as a flowering repressor. This high-quality genome assembly of ‘Deyangshi’ provides an essential genomic resource for the Diospyros genus, particularly for breeding programs focused on developing early-flowering persimmon varieties.

Figures