A haplotype-resolved lychee pangenome uncovers structural and haplotype variations associated with flowering time divergence and fruit sugar composition.

A haplotype-resolved lychee pangenome identifies a ~10 kb promoter structural variant in LcFT3 that is linked to flowering time divergence via CO-NF transcriptional regulation.

• Why it matters: Flowering and fruit sugar traits vary widely in lychee, but the genomic variants—especially structural and haplotype-level changes—underlying that diversity are not well resolved.
• What they did: The study reassembled and curated the lychee reference genome, built haplotype-resolved genomes for 12 accessions, and constructed the first lychee pangenome, then integrated it with resequencing from 314 accessions.
• The result: It revealed extensive structural and gene copy number variation across lychee and found LcSAI locus SVs significantly associated with fruit sugar content, with combined coding and cis-regulatory effects on enzyme activity and gene expression.

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