APPLICATION ARTICLE A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae Johanna R. Jantzen1,2,6* , Prabha Amarasinghe1,2* , Ryan A. Folk3 , Marcelo Reginato4,5 , Fabian A. Michelangeli4 , Douglas E. Soltis1,2 , Nico Cellinese2† , and Pamela S. Soltis2† Manuscript received 9 September 2019; revision accepted PREMISE: Putatively single-copy nuclear (SCN) loci, which are identified using genomic 20 December 2019. resources of closely related species, are ideal for phylogenomic inference. However, suitable 1 Department of Biology, University of Florida, Gainesville, Florida genomic resources are not available for many clades, including Melastomataceae. We 32611, USA introduce a versatile approach to identify SCN loci for clades with few genomic resources 2 Florida Museum of Natural History, University of Florida, and use it to develop probes for target enrichment in the distantly related Memecylon and Gainesville, Florida 32611, USA Tibouchina (Melastomataceae). 3 Department of Biological Sciences, Mississippi State University, Starkville, Mississippi 39762, USA METHODS: We present a two-tiered pipeline. First, we identified putatively SCN loci using 4 Institute of Systematic Botany, The New York Botanical Garden, MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Bronx, New York 10458, USA Published loci and genes of functional significance were then added (384 total loci). Second, 5 Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio using HybPiper, we retrieved 689 homologous template sequences for these loci using Grande do Sul 90040-060, Brazil genome-skimming data from within the focal clades. 6Author for correspondence:
[email protected] *These authors contributed equally to this work.