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

Dodders (Cuscuta spp.) are obligate parasitic plants that have lost a large portion of their photosynthetic genes but gained host genes through parasitism-mediated horizontal gene transfer. Their genetic complexity of speciation is partly clarified at the genome level. 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 a distinct section of the subgenus Grammica. The relatively low completeness of eudicot Benchmarking Universal Single-Copy Orthologs genes (~87%) indicates progressive gene loss after evolution of the parasitic lifestyle due to release from functional constraints. Comparative genomics analyses reveal that the genome sizes of the two species differ significantly, even though they have the same number of chromosomes and allopolyploidy via independent hybridization involving different ancient parents. Various genomic rearrangements have likely contributed to the genomic diversity of the two lineages, which partly share habitats, including (i) gene gain and loss events, (ii) homoeologous recombination between two subgenomes, and (iii) lineage-specific transposable element dynamics. Our findings not only provide a genomic basis for surveying parental species for allopolyploidization but also enhance our understanding of the unique speciation of parasitic dodders through allopolyploidization.