Chromosome-level genome assembly of the Australian Chenopodium trigonon reveals a new subgenome type

The genus Chenopodium comprises a diverse assemblage of diploid and polyploid species distributed worldwide, yet Australian taxa remain genomically undercharacterized. Here, we report a chromosome-level genome assembly of Chenopodium trigonon , an Australian halophytic tetraploid. Using 23.6 Gb of PacBio HiFi and Hi-C data, we generated an 830.9 Mb assembly with high contiguity (scaffold N50 = 45.9 Mb), 99.2% BUSCO completeness, and near-complete chromosomal representation (n = 18). Comparative synteny, orthology, and repeat landscape analyses were performed to investigate subgenome composition, evolutionary relationships, and genome evolution. Our analyses revealed that C. trigonon is an allotetraploid composed of an A subgenome and a subgenome belonging to a deeply divergent G/H-like lineage that we designate as a novel “I” genome, showing pronounced structural divergence relative to the G and H subgenomes. Both subgenomes form sister groups to other members of their respective clades and exhibit extended branch lengths, consistent with an independent polyploidization event relative to C. sosnowskyi . Repeat landscape analyses demonstrated that genome size differences between species are largely driven by differential LTR retrotransposon accumulation, with distinct temporal and compositional dynamics across subgenomes. Comparative read-mapping of the Australian octoploid C. baccatum further indicated predominant A and I ancestry (putative AAAAIIII), suggesting that an ancestral A–I genomic combination may underlie diversification of Chenopodium in Australia.