2.10 Gene family cluster identification and phylogenetic analysis
Nine species (Arabidopsis thaliana , Citrus sinensis, Juglans regia , Malus domestica , Olea europaea ,Oryza sativa , Populus euphratica , Quercus robur , and Chinese walnut) were selected for comparative genome analysis. All-versus-all BLASTP (Altschul et al., 1990) search results (Evalue = 1e−5) were used for gene family construction using OrthoMCL (Fischer et al., 2011). A maximum likelihood (ML) phylogenetic tree was constructed using RAxML v8.2.12 by conducting 1,000 bootstrap replicates. Species divergence times were estimated using PAML v4.5 software and MCMCtree (Yang, 2007) with the following parameters: 10,000 burn-ins, sample-frequency=2, and sample-number=100,000. We applied fossil calibration points to inform the species divergence time using Timetree (http://www.timetree.org/). CAFE v2.2 (Computational Analysis of gene Family Evolution) (Bie et al., 2006) was used to assess the expansions and contractions of orthologous gene families among all nine plant genomes based on the consensus phylogeny.