Phylogenomic evidence reveals non-monophyly of Paepalanthoideae and challenges the broad concept of Paepalanthus (Eriocaulaceae)

Sequence aligment of target capture sequences of multiple species of Eriocaulaceae. Alignments are names after the genes in the Angiosperms353 bait set. Please see the related publication for details about voucher specimens. Methods: The demultiplexed raw reads from sequencing were subjected to quality filtering and trimming using the default settings of the “clean” function in Captus v1.3.2 (Ortiz & al., 2023), where average PHRED quality score threshold of 13 for trailing reads and 16 for entire reads were applied. The “assemble” function was used to assemble paired reads into contigs. Then, the “extract” function was used to capture only the reference sequence set of nuclear proteins contained in the “Mega353” file (McLay & al., 2021) from the assemblies. The “align” function aligned the extracted loci using MAFFT’s automatic selection based on the amount of data from complete gene sequences (exons + introns) with flanking upstream and downstream base pairs using the “GF” argument. Paralogs were filtered using “naive” option.