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.