OrthoFinder Version 2.5.4 (Emms and Kelly, 2019 (link)) was employed to construct the orthogroups for the transcriptomes with default settings. We gathered three independent datasets to reconstruct the phylogeny of Pinaceae genera: 1) a dataset of 319 single-copy orthologous genes (SCOGs) generated from 15 Pinaceae plant transcriptomes; 2) a dataset of 120 SCOGs of 16 taxa, including 15 Pinaceae species and one Cycadaceae species (outgroup); 3) and another dataset of 54 SCOGs derived from 18 taxa, including 15 Pinaceae plants and three outgroups (an Araucariaceae plant, a Cupressaceae plant and a Cycadaceae plant). TranslatorX (Abascal et al., 2010 (link)) was used for multiple gene alignments based on codon (nt), codon 1st+2nd (nt12) and amino acid (aa) sequences with the local version (command: perl translatorx_vLocal.pl -i gene.fa -o gene.out -p M -t F -w 1 -c 1 -g “-b2 = 0.75 -b3 = 8 -b4 = 5 -b5=h -b6=y”). The maximum likelihood (ML) approach was used to build a concatenated tree for the different sequences of each dataset using IQ-TREE (Nguyen et al., 2015 (link)). ASTRAL (Zhang et al., 2018 (link)) was used to derive a coalescent tree for the different sequences of each dataset.
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