A gap-free telomere-to-telomere genome of the purple-pericarp rice landrace Mojiang ZN65 resolves transposon-driven structural variation at the pericarp-pigmentation loci

Pigmented rice landraces are prized for their anthocyanin-accumulating pericarp, yet the repeat-rich regulatory alleles that govern pigmentation are poorly resolved in draft assemblies. Here we report a gap-free, telomere-to-telomere (T2T) genome of Mojiang purple rice (ZN65), a glutinous purple-pericarp Hani landrace from Yunnan, China. The 395.1-Mb assembly comprises twelve gap-free chromosomes with all 24 telomeres, all 12 centromeres and the 45S/5S ribosomal DNA arrays resolved (contig N50 32.35 Mb; Merqury QV 53.6; 99.6% BUSCO); we annotated 42,090 protein-coding genes, with transposable elements occupying 56.6% of the genome. Against the japonica reference Nipponbare we identified 1,045,956 single-nucleotide variants, 121 inversions and 449 translocations; ZN65 is larger on every chromosome (~22 Mb cumulative excess), reflecting lineage-specific retrotransposon expansion (26.9 Mb of LTR/Gypsy within 73.3 Mb of ZN65-specific sequence), and falls in the indica group. The flavonoid pathway is complete and copy-number-conserved (100 genes), so pigmentation maps to regulators: OsC1/Kala3 is conserved, whereas Kala4/OsB2, Kala1/OsDFR and Rc each carry transposon-associated structural variation. ZN65 encodes a functional pigmentation-allele complement - most diagnostically a full-length Rc with an intact bHLH domain, unlike the truncated rc allele of white Nipponbare. At Kala4/OsB2, ZN65 carries a long-read-validated retrotransposon architecture, including a ZN65-specific proximal-promoter insertion absent across a seven-genome panel - a candidate, lineage-specific realization of the black-rice gain-of-function mechanism, distinct from the canonical tandem-duplication allele. This T2T resource and its pigmentation-locus haplotypes provide a foundation for the functional study and molecular breeding of pigmented rice.