Supplemental Material for Cerda-Herrera et al., 2025

We present the first chromosome-level genome assembly and annotation for the genus <em>Cuscuta</em>, a twining and leafless parasitic plant of the morning glory family (Convolvulaceae). <em>C. campestris</em>, the study species, is a widely studied model parasite, due in part to its worldwide occurrence as a weed of agricultural and natural plant communities. The species has served as a model parasite for studies of parasite biology, haustorium development, growth responses to chemical and light stimuli, gene content and expression, horizontal gene transfer, interspecies RNA movement, and has a recently developed transformation system. The 505 Mb (1C) genome is assembled into 31 chromosomes and supports annotation of 47,199 protein-coding genes, 214 small RNA loci (including 146 haustoria-specific miRNAs), and 3,238 interspecies mobile mRNA loci. <em>C. campestris </em>is a recent tetraploid with a high retention of duplicated genes and chromosomes, and less than 8% nucleotide divergence between homoeologous chromosomes. We also show that transformation of <em>C. campestris</em> with the RUBY marker system allows visualization of transformed <em>Cuscuta</em>-derived fluorescent mobile molecules that have entered the host stem. This genome will be of value for researchers performing basic research in a wide range of molecular, developmental, population and evolutionary biology, as well as a research tool for studying interspecies mobile molecules, generating genetic markers for species and genotype identification, and for the development of highly specific herbicides.