A well‐resolved phylogeny of Cuscuta subgenus Monogynella based on data drawn from all three plant genomes

PREMISE: Cuscuta (dodders) consists of ~200 species circumscribed into four subgenera (Monogynella, Cuscuta, Pachystigma, and Grammica) and is the only parasitic genus in Convolvulaceae (the morning-glory family). This group shows a significant diversity in plastid functionality and represents a rare mixotrophic system among parasitic plants. Apart from a few placeholders in broadscale phylogenies, subg. Monogynella had not been extensively examined until a recent molecular systematics study. Despite this effort, a few lineages still remained poorly resolved and some backbone relationships lacked support. METHODS: To obtain greater resolution and support for the phylogeny alongside studying the effect of hemiparasitism on different organellar genomes, we selected 31 samples, chosen to represent the phylogenetic diversity of each clade, and sequenced them using high-throughput sequencing. We assembled plastid genomes and retrieved mitochondrial genes and nuclear ribosomal arrays (NRAs) for phylogenomic analyses. RESULTS: Plastomes in this subgenus show similar lengths and gene composition and retain the bulk of photosynthesis genes. About 33 mitochondrial genes were recovered from assemblies and are more conserved in comparison to plastid genes. In addition, complete NRAs were also found to be well maintained. The members of subg. Monogynella show no evidence of hybridization. Trees obtained from all three matrices corroborate previously published molecular phylogenies with increased resolution and backbone support across the board. CONCLUSIONS: These results characterize the state of the organellar genomes and particularly plastomes in subg. Monogynella, bridging the gap in this field of study of Cuscuta and allowing us to compare these patterns across other heterotrophic lineages.