Triangle of U Flowering Locus C (FLC) Phylogenetic Tree

Alignment file and Newick tree for Flowering Locus C (FLC) orthologs among the Triangle of U species. To investigate orthologs among the Triangle of U species, phylogenetic trees were constructed for three agriculturally important genes: Flowering Locus C (FLC), Fatty Acyl Elongase 1 (FAE1) and Fatty Acyl-CoA Reductase 1 (FAR1). We aligned the coding sequences and peptide sequences using the MUSCLE alignment software (Edgar, 2004). Next, each alignment was adjusted using PAL2NAL (Suyama et al., 2006) according to the protein sequence alignments. We used a single matrix comprised of the aligned sequences to determine the best-fit nucleotide substitution model under a Bayesian information criterion (BIC) in IQ-TREE (Nguyen et al., 2015). Lastly, the phylogenetic trees were reconstructed using RAxML under the GTR + CAT model with 1,000 bootstrap replicates.