Wild genomes reveal apricot’s hidden structural diversity
Nanjing Agricultural University The Academy of Science
image:
Evolutionary relationships among assemblies. A. Distance tree of selected Armeniaca genome assemblies. This tree aims to define an order for pangenome graph construction (see methods) and, as a consequence, is rooted on the selected reference genome Rojo_HCUR and not outgroups. Wherever possible, individual haplotypes are maintained as distinct leaves (labels H1 and H2). B. Global synteny among all of chromosome 1. Horizontal lines represent chromosome length, and colored vertical blocks represent all rearrangements detected between consecutive chromosome pairs.
view moreCredit: Horticulture Research
Apricot breeding has long depended on a narrow genomic view, leaving much of the variation preserved in wild relatives outside the frame. A phylogeny-guided pangenome now brings that hidden diversity into focus across domesticated and wild members of the Armeniaca section. By integrating chromosome-scale assemblies from common, Siberian, and Manchurian apricots, the study captured millions of small variants and more than half a million structural changes that a single reference genome can miss. It also revealed how distant lineages enlarge the accessible gene pool and how transposable elements reshape regions near genes. The resource offers a stronger foundation for investigating domestication, adaptation, dormancy, and future apricot improvement.
Cultivated apricot, Prunus armeniaca, emerged through at least two domestication routes from Central Asia before spreading toward China and the Mediterranean. Yet most population studies still compare diverse plants with one reference sequence, creating reference bias and obscuring structural variants, copy-number variants, and lineage-specific DNA. Pangenomes can represent many genomes together, but most graph-building tools were developed for variation within a single species. Extending these tools across closely related, interfertile taxa introduces additional challenges because evolutionary distance can complicate genome alignment and variant detection. Based on these challenges, deeper investigation into a phylogeny-aware, cross-taxon pangenome for apricot and its wild relatives is needed.
A research team led by the French National Research Institute for Agriculture, Food and Environment (INRAE) at Université de Bordeaux and Université de Toulouse, with collaborators from Université de Rouen Normandie, Université Paris-Saclay, the French National Centre for Scientific Research (CNRS), AgroParisTech, and New York University Abu Dhabi, published (DOI: 10.1093/hr/uhag104) the study in Horticulture Research on March 27, 2026. The researchers constructed a chromosome-level pangenome graph from 25 curated assemblies representing Prunus armeniaca, P. sibirica, P. mandshurica, and interspecific hybrids, then assessed genomic diversity, read mapping, and dormancy-associated structural variation.
The researchers first assembled a dataset of 32 Prunus genomes, including seven generated for this study, and corrected chromosome labels, orientations, and other assembly inconsistencies before selecting 25 assemblies for graph construction. Guided by evolutionary relationships, the graph identified approximately 25 million single-nucleotide polymorphisms (SNPs) and more than 537,000 insertions and deletions, a major class of structural variants (SVs). Closely related European genomes added progressively less new sequence, whereas wild Central Asian, Chinese, Siberian, and Manchurian material contributed substantial accessory and private regions. The team also detected 42,679 transposable elements (TEs) within graph-derived insertions and deletions. About three quarters occurred within 2.6 kilobases upstream or downstream of a start codon, supporting a possible role in gene regulation while suggesting selection against insertions directly at start sites. Mapping 322 short-read samples to the graph recovered 0.5% to 9.2% more reads than mapping them to the single Rojo_HCUR reference. As a case study, the researchers resolved four large variants across the Dormancy-Associated MADS-box (DAM) gene cluster—MADS refers to MCM1, AGAMOUS, DEFICIENS, and serum response factor—and used polymerase chain reaction (PCR) assays to test an insertion between DAM2 and DAM3. The analysis also exposed a probable genome-assembly error at this locus. This broader representation reduced the bias created by a single genomic template.
The authors said the pangenome shows why one cultivated genome cannot serve as a complete standard for apricot diversity. They said the largest additions came from evolutionary groups that are often underrepresented in breeding collections, particularly wild and more distant relatives. In their view, the close relationship between transposable elements and structural variation offers a plausible route through which genome architecture may influence nearby genes and plant traits. They also emphasized that careful assembly curation is essential, because errors in chromosome structure or labeling can otherwise be mistaken for genuine biological variation in graph-based analyses.
The pangenome can support genome-wide association studies (GWAS) that evaluate structural variants alongside conventional SNP markers, helping researchers prioritize genomic regions connected with bud dormancy, flowering, environmental adaptation, and other complex traits. These links will still require broader phenotyping and functional validation before they can guide selection directly. The resource can also make future sequencing more strategic by showing which evolutionary groups contribute the greatest amounts of previously unrepresented DNA. For breeders, wild apricot relatives may provide alleles and structural variants that are scarce in cultivated germplasm. Beyond apricot, the phylogeny-driven workflow offers a practical model for constructing cross-taxon graph references in other perennial fruit trees with diverse, interfertile wild relatives.
###
References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhag104
Funding information
This work was supported by a PhD fellowship from the French Ministry of Higher Education and Research (MNSER) and Université de Bordeaux, an apprenticeship grant from the French National Research Institute for Agriculture, Food and Environment (INRAE), the European Union’s Horizon Europe FRUITDIV project (Grant No. 101133964), and the France 2030 AGRODIV program administered by the French National Research Agency (ANR-22-PEAE-0005-AgroDiv). The de novo assemblies of wild Armeniaca genomes were additionally supported by the University of Bordeaux WOODYSV project (2020–2022) and the ANR JCJC PLEASURE project (ANR-21-CE20-0005). The BReIF e-infrastructure was funded under Grant No. ANR-22-PEAE-00014-BREiF.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
Journal
Horticulture Research
Subject of Research
Not applicable
Article Title
Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species
No comments:
Post a Comment