Most plant genome assemblies are haploid representations—they collapse two distinct parental chromosomes into a single, chimeric sequence. For highly heterozygous, clonally propagated crops like pineapple, this approach discards vast amounts of allelic diversity preserved through millennia of vegetative propagation. Previous assemblies of ‘Smooth Cayenne’ could not resolve large inversions, creating spurious inter‑chromosomal linkages that misled genome‑wide association studies (GWAS) and genomic prediction models. Due to these limitations, a truly phased, telomere‑to‑telomere (T2T) reference has remained out of reach—until now.
Now, an international team led by researchers from Fujian Normal University, The University of Queensland, and Murdoch University reports the first haplotype‑resolved, T2T genome assembly for pineapple. Published (DOI: 10.1093/hr/uhag189) on May 8, 2026, in Horticulture Research, the study provides a complete, phased reference for the pre‑Columbian cultivar ‘Smooth Cayenne’ (F180). Using PacBio high‑fidelity (HiFi) long‑read sequencing and high‑throughput chromosome conformation capture (Hi‑C), the team resolved both haplotypes into 25 chromosomes each, identifying all 50 centromeres and 44 of 50 telomeres.
The phased assembly revealed that inversions are far more than passive genomic features—they actively shape recombination landscapes. On chromosome 20, a 1.3‑megabase paracentric inversion forms a strict recombination coldspot: not a single crossover was detected within its boundaries across 374 F₁ progeny. In inversion heterozygotes, single crossovers produce dicentric bridges and acentric fragments, leading to inviable gametes and effectively locking ~170 genes into a single inherited haploblock. By contrast, a 6‑megabase pericentric inversion on chromosome 24 still permits gene flow, likely through short double crossovers that restore euploidy. Although recombination within this region is reduced compared to the rest of the chromosome, it is not abolished—demonstrating that chromosomal context, not size alone, determines whether an inversion acts as a genetic fortress or a leaky barrier. When the same 11,879 Diversity Arrays Technology sequencing (DArTseq) markers were re‑anchored to the phased F180 reference, spurious inter‑chromosomal linkages dropped from over 240 to fewer than 100, providing cleaner baselines for GWAS and genomic prediction. The study also uncovered allele‑specific expression genes (ASEGs) such as AcSBT1.7 and AcUFC, where transposable element insertions in promoter regions suppress one allele’s expression—offering mechanistic clues to how heterosis is maintained in a clonal crop.
The authors said: “What surprised us most was that two large inversions of very different sizes behave in completely opposite ways. The smaller one on chromosome 20 completely shuts down recombination, while the much larger one on chromosome 24 still allows genetic exchange. This tells us that the genomic context—where an inversion sits and what it carries—matters as much as its size. For breeders, this means some inversions trap valuable gene combinations forever, while others can still be reshuffled. Understanding these differences is the first step toward designing smarter breeding strategies.”
The findings have immediate implications for pineapple breeding and beyond. The phased F180 assembly provides a high‑quality reference that resolves SVs previously hidden in collapsed genomes, enabling more precise mapping of traits such as flowering asynchrony, disease resistance, and climatic resilience. The reduction in false inter‑chromosomal linkage disequilibrium translates directly into cleaner GWAS signals and more accurate genomic prediction models. Moreover, the contrasting recombination behaviours of the two inversions offer a framework for understanding how structural variation shapes haplotype inheritance in other clonally propagated perennials—from mango to citrus to avocado. As breeding programmes increasingly adopt genomic selection, phased, T2T assemblies will be essential for capturing the full allelic diversity that clonal propagation has preserved for millennia.
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References
DOI
10.1093/hr/uhag189
Original Source URL
https://doi.org/10.1093/hr/uhag189
Funding information
This work was supported by Hort Innovation, "Building an Advanced Genomics Platform for Australian Horticulture (AS21006)".
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.