Whole protein-coding gene repertoires from 14 plant genomes including G. elata, A. comosus 10, A. trichopoda 45, O. sativa (phytozome v10), Z. mays (phytozomev10), D. officinale9, P. equestris7, Elaeis oleifera60, A. thaliana (phytozomev10), V. vinifera (phytozomev10), Populus trichocarpa (JGI), Glycine max (phytozomev10), Picea abies61, Physcomitrella patens (ASM242v1) were used to construct a global gene family classification. To remove redundancy caused by alternative splicing variations, we retained only gene models at each gene locus that encoded the longest protein sequence. To exclude putative fragmented genes, genes encoding protein sequences shorter than 50 amino acids were filtered out. All-against-all BLASTp was employed to identity the similarities between filtered protein sequences in these species with an E-value cut-off of 1e−7. The OrthoMCL62 method was used to cluster genes from these different species into gene families with the parameter of “-inflation 1.5”.