4.1. Sampling for the Phylogenetic Analyses of Class I KNOX Genes

To gain a more detailed evolutionary history of Class I KNOX in ferns and to discover the putative Elaphoglossum Class I KNOX gene copies for our expression studies, we obtained representative species across the fern and lycophyte phylogeny from publicly available databases and by cloning. We included Class I KNOX genes previously published from the lycophytes Selaginella krausiana [10], Huperzia selago and Isoetes tegetiformans [87], and Lycopodium deuterodensum [88]; from the ferns Ceratopteris richardii [32], Elaphoglossum peltatum f. peltatum [33], and Equisetum diffusum [88]. We got these sequences from GenBank, the 1KP plant transcriptome project (http://www.onekp.com, accessed May 2018) databases, or directly from the published papers. BLAST similarity searches (Altschul et al., 1990) in the lycophyte Selaginella moellendorffii genome available in Phytozome (https://phytozome.jgi.doe.gov, last accessed May 2018) were used to identify Class I KNOX copies in S. moellendorffii. BLAST searches were also conducted in the fern genomes of Azolla filiculoides and Salvinia cucullata, available in Fernbase (https://www.fernbase.org/, last accessed May 2019). Further lycophyte and fern sequences were obtained using degenerate primers previously published [33]. For the phylogenetic analyses, published sequences from GenBank for the other lineages of vascular plants (gymnosperms and angiosperms) were also included. Class I KNOX Physcomitrium patens sequences available at GenBank were used as outgroups and to root the trees. A list of all sampled species, provenance, and accession numbers is provided in Appendix A (these will be provided during review).