Monotropoid Ericaceae 102-locus nuclear sequences matrices and plastid locus sequence matrix

Monotropoideae (Ericaceae) is a wholly leafless and holomycotrophic group of primarily temperate herbs with centers of diversity in western North America and east Asia.   The eleven genera are structurally diverse and also vegetatively reduced, making relationships difficult to assess based on morphology.  Previous molecular analyses have focused primarily on segments of the ribosomal RNA repeat and yielded sometimes conflicting topologies.  We employed a genomic sampling approach to obtain 102 nuclear loci and plastid coding loci for nine of the genera, as well as sampling ITS-26S and plastid rps2 for a broader set of accessions via PCR and Sanger sequencing Data filtering for character completeness had a clear effect on relationships and branch support.  Nuclear and plastid loci agree on a topology that resolves Allotropa and Hemitomes as sisters and Monotropsis sister to Eremotropa+Monotropa+Monotropastrum, relationships that were unclear from previous analyses.  Hypopitys should be ..., Data were collected using Illumina sequencing and a low-coverage genome skimming approach., , # Monotropoid Ericaceae 102-locus nuclear sequences matrices and plastid locus sequence matrix

[https://doi.org/10.5061/dryad.7h44j1017](https://doi.org/10.5061/dryad.7h44j1017)

These matrices were derived from genome-skimming runs using Illumina sequencing technology. After the pools of reads were obtained, they were mapped to Angiosperm353 target sequences from Monotropa uniflora, which were obtained from the supplementary data in the paper that described that probe set (Johnson et al., 2019, Systematic Biology 68: 594-606). This allowed us to recover sequences from our reads that matched the Angiosperm353 orthologs. 102 of these were assembled into a concatenated dataset for analysis of monotropoid relationships and filtered to different levels of individual base-position completeness: 100% complete, 80% complete, 50% complete, and unfiltered (all data included). These matrices are provided in NEXUS format.

We also assembled plastid genomes from the skimming reads and de novo mapp...