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Abstract Heterotrophic plants are among the most recalcitrant from a systematics perspective because of reduced morphological and genomic features, and often extreme substitution rate heterogeneity. The orchid subtribe Calypsoinae exemplifies this, containing several lineages that have lost leaves and photosynthesis. In particular, relationships of the leafy Asian Oreorchis and the leafless American Corallorhiza have been contentious. Here we used nuclear sequence capture to resolve relationships within Calypsoinae and addressed the monophyly of Corallorhiza and Oreorchis, for which previous studies have highlighted conflicting patterns of monophyly or paraphyly, depending on the data analysed. Nuclear analyses provided strong support for a monophyletic Corallorhiza and paraphyletic Oreorchis, the latter with two strongly supported clades. As in previous studies, plastid analyses recovered strongly supported paraphyletic assemblages for both genera. Topology tests using plastid and nuclear relationships and data rejected the constrained topologies, further revealing strong cytonuclear conflict. Network-based analyses revealed a lack of evidence for hybridization, suggesting incomplete lineage sorting associated with biological and historical factors have driven intergenomic conflict. Additionally, we found that loci identified as putatively lost in holomycotrophic Corallorhiza species are functionally enriched for organellar functions. The study provides a strong case for the resurrection of Kitigorchis as the sister of Corallorhiza, with two species, Kitigorchis erythrochrysea and Kitigorchis indica, and highlights the challenges associated with phylogenetics of lineages containing mycoheterotrophs. 

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.