Defense response GOs to four linkages of natural enemies
We totally obtained 14471, 23949, 877, and 4797 genes from 99 tree species annotated as the four GOs (defense response to fungus, bacterium, insect and virus) respectively. For each GO, we obtained 129, 216, 6 and 45 homologous gene clusters contained in at least ten species. A chord diagram was drawn to show the mean copy number of the four GOs in top ten families with high seedling density (Fig 1). There were 51 clusters shared by GOs defense response to fungus and bacterium, while 78 (60.5%) and 161 (74.5%) clusters were specific to the two GOs respectively (Fig. 2). By comparison, the GO defense response to bacterium shared only four clusters with GO defense response to virus and only one cluster with GO defense response to insect. Moreover, The GOs defense response to fungus, bacterium and virus also share only one cluster (Fig.2).
Among these homologous gene clusters related to defense responses, we found kinases acting as sentinels in signaling pathway in pathogen resistance, transcription factors regulating plant immunity, enzymes in biosynthesis or RNA silencing, one transmembrane protein, and one ribonucleoprotein in defense response to virus (Table S2). Four out of the top six gene clusters were shared between defense response to fungus and bacterium, including three transcription factors (MYB44 ,WRKY33 , and WRKY40 ) and one receptor kinase (ERECTA ). FER and RD21A were also found involved in defense response to fungal pathogens. PBS1 and SNC1 with the function of protein kinase and disease resistance protein respectively, were in the top six clusters in defense responses to bacterium. As for defense response to insect, two gene clusters with the function of transcription factor (CAF1-9 and ERF18 ) associated with rapid responses to insects and four enzymes (PAD4 , LIP2 , CYP81D11 , and CYP94B3) involved in plant hormone jasmonate (JA) related defenses or lipase modulating leaf senescence were found. Among the gene clusters associated with defense response to virus, two gene clusters (AGO2 and DCL3 ) have the function of antiviral RNA silencing, and SAMHD1 homolog may act as a host restriction factor.
The heap map showed that the functional CNV dissimilarity of defense responses was lineage specific, and species in the same genus or family were always clustered together (Fig. S1). At least one of the first two principal coordinates of functional CNVs species pair-wised distance matrix for each defense response showed significant phylogenetic signal (Table S3).