Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae

PREMISE: Information on orthologous groups of genes, their sequence variability, and annotation is required for project design in phylogenetic reconstruction. This resource is unavailable for the flowering plant family Acanthaceae (>4000 species). METHODS: We compared transcriptome sequences spanning the extant diversity of Acanthaceae in order to provide a set of orthologous low‐copy nuclear genes and assess their utility for reconstructing phylogenetic relationships within this group of plants. RESULTS: We present new transcriptome assemblies for eight species representing all major clades of Acanthaceae. The assemblies of five of these species are entirely based on new sequence data. Of these five species, three are from subfamilies for which no genomic resources were previously available (Nelsonioideae and Thunbergioideae). These five new transcriptomes are more complete than all others from public databases. Furthermore, we provide alignments with sequence information, annotation, and statistics for potential phylogenetic utility of 1619 orthologous low‐copy nuclear markers. DISCUSSION: Our method of inferring assemblies from multiple pooled tissue samples delivers more complete transcriptomes than any available ones from Acanthaceae. We make available to the community new resources (e.g., sequence information, variability, and annotation of orthologous low‐copy nuclear genes) that will help phylogenetic reconstruction in Acanthaceae.