Figure 2. Expansion of PIM1 through segmental duplication. (A) Phylogenetic relationship and motif composition of 143 duplicated PIM proteins identified with complete protein kinase domain in tree sparrow genome and PIM family members from other species (2 of chicken, 3 of human and 6 of zebra finch). The inner layer is a maximum-likelihood tree of the total 154 PIM proteins. All PIM1 of tree sparrow are divided into 2 subgroups based on the phylogenetic tree. The outer layer is the distribution of the conserved motifs in PIM proteins and the 10 motifs are represented by boxes with different colors. The PIM1 from same subgroup have more similar motifs. (B) Chromosomal distribution and segmental duplication events of 7 expanded gene families in tree sparrow genome. The expansion of PIM is derived from segmental duplication of genomic regions contained PIM and other 6 families includingC2H2ZNF , OR , PAK ,MROH , HYDIN and ITPRIPL . The distribution density of these 7 families on each chromosome is shown in the form of heatmap and the scale on the left represented the length of chromosomes. The smaller chromosomes 18-36 contained most of the duplicated regions are zoomed in and the different degree of expansion of 7 families are shown in the bottom bar chart. (C) The distribution of 7 expanded gene families and LTR retrotransposons in chromosomes 18-36. The duplicate gene number is represented by the red line when LTR retrotransposons density is represented by the black line. The distribution of duplicate gene is consistent with the density of LTR retrotransposons. (D) Expansion of PIM family in other avian lineages. Box plot for the numbers of PIM family members in 12 avian orders. Expansion ofPIM occurred in three orders which are shadowed in yellow.