Chromosome-scale genome assemblies of two allopolyploid <em>Cuscuta</em> species uncover genomic signatures of parasitic lifestyle and polyploid evolution

Dodders (Cuscuta spp.) are obligate parasitic plants that have lost a large portion of photosynthetic genes but gained host genes through parasitism-mediated horizontal gene transfer. Their migration across the world has contributed to the complexity of speciation via geographic isolation. Here, we report the de novo genome assemblies of two phylogenetically distinct dodders: Cuscuta campestris (2n = 4x = 60) and Cuscuta chinensis (2n = 4x = 60), which are classified into Clade B and Clade H of subgenus Grammica, respectively. Relatively low completeness of Benchmarking Universal Single-Copy Orthologs genes (ca. 87%) indicated progressive gene loss after evolution of the parasitic lifestyle due to release from functional constraints such as photosynthesis and organ development. Comparative genomics analyses revealed that the genome size of each species differs significantly, despite having the same cytotype and allopolyploidy, through independent hybridization involving different ancient parents. Various genomic rearrangements have likely contributed to the genomic diversity and sexual isolation of the two lineages, which partly share habitats, including (1) gene gain and loss events, (2) homoeologous recombination between two subgenomes, and (3) lineage-specific proliferation of transposable elements. Our findings not only provide a genomic basis for surveying parental species for allopolyploidization but also enhance understanding of the unique speciation of parasitic dodders through these chromosomal events.