Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data

Abstract

The utility of 18S and 26S in broad phylogenetic analyses has been much maligned due in large part to the low signal in both genes. However, few analyses have employed complete 26S rDNA sequences over a broad range of taxa, and most alignments of the two genes are done de novo, without taking into account the secondary structure of the two rRNA genes. Here we mine next-generation sequence data to compile large matrices (429 taxa) of complete 18S + 26S gene sequences, and we compare both de novo alignment methods with curated alignments done by eye that take into account secondary structure and hard-to-align regions (profile alignments). The combined 18S + 26S topology is overall very similar to recently published gene trees for the angiosperms based on three or more genes. Overall support for the backbone or framework of the combined tree is low (bootstrap support below 50%). Few major clades have bootstrap support above 50%. Most well-supported clades are tip clades (families and orders sensu APG III 200...