Expansion of PIM family by tandem and segmental duplication of PIM1
PIM1 , a member of the PIM gene family composed of three single-copy genes (PIM1, PIM2, PIM3 ) and highly evolutionarily conserved in multicellular organism, was originally identified as a common proviral insertion site for the Moloney murine leukemia virus (Selten et al., 1985) and has been known as a proto-oncogene and implicated in the control of cancer cell proliferation, migration and apoptosis (Narlik-Grassow et al., 2014). In contrast to other amniotic genomes (including chicken) that harbor only single copy of PIM1gene, large expansion of PIM1 which have been reported in zebra finch (Taeniopygia guttata ) (Kong et al., 2010), another species of songbird, is also found in tree sparrow when PIM3 keeps one single copy. Out of a total of 449 initially predicted PIM1genes, only 142 are found to be complete for the conserved protein kinase domain which related with the protein kinase catalytic activity. To deduce the evolutionary relationship of the PIM family, we construct a phylogenetic tree containing 154 PIM (2 of chicken, 3 of human, 6 of zebra finch and 143 of tree sparrow) proteins and divided the expanded PIM1 genes of tree sparrow into 2 subgroups based on the constructed phylogenetic tree (Figure 2A). All subgroup I PIM1 proteins are found to have similar conserved motifs (motif 6-10) with the chicken and human PIM1 when subgroup II PIM1 have at most 5 excess motifs (motif 1-5) which also appear in the zebra finch (Figure 2A; Figure S5). The structural variation of subgroup II PIM1 proteins may be derived from an insertion event during duplication.
Notably, besides the structural difference, the two subgroups show different chromosomal distribution pattern and duplication mechanism. All subgroup I PIM1 are centered in chromosome 7 and 24 when subgroup II have more decentralized distribution (Table S7). The centered distribution pattern of subgroup I is mainly owing to the tandem duplication events involved in the expansion of subgroup IPIM1 genes and the more dispersed subgroup II PIM1 genes are derived from segmental duplication (Figure S6). The dispersed duplicates of PIM1 are noticed to be always adjacent to genes of several other families including C2H2zinc finger (C2H2ZNF ) protein, olfactory receptor (OR ), p21-activated kinase (PAK ), maestro heat-like repeat containing protein family member (MROH ), hydrocephalus-inducing protein homolog (HYDIN ) and inositol 1,4,5-trisphosphate receptor-interacting protein-like (ITPRIPL ) which result in these 6 gene families expand simultaneously but at different degree in tree sparrow genome (Figure 2B; Figure S6). Furthermore, we find that the genomic regions contained these 7 families mainly distribute across chromosomes Z and 18-36, and these regions also contain high density of long terminal repeat (LTR) retrotransposons (Figure 2C; Figure S7), the same distribution pattern of these 7 families members and LTR retrotransposons may indicate that the expansion of these 7 families and LTR retrotransposons happened in tree sparrow genome simultaneously. Based on these results, we assume that large, interspersed segmental duplication of genomic regions contained random members of these 7 gene families occurred multiple times at different time points during evolution, and these replication events may be the strong driving force of the evolution of tree sparrow genome.
As so far, the expansion events of PIM1 are only found in passerine (zebra finch and tree sparrow). To find out if the expansion of PIM1 is songbird-specific, the PIM gene family members are identified and counted for all available avian genome in Ensembl, including 47 species covered 12 avian orders (Table S8). By comparing the number of PIM1 in the 47 genomes, the expansion ofPIM1 is detected in 18 species of 3 orders (Figure 2C; Table S9). This result show that the expansion of PIM gene family caused by duplicated PIM1 genes occurred not only in the order Passeriformes, but also in Psittaciformes and Strigiformes (Figure 2C) which may indicate the PIM1 genes duplicate independently in several avian lineages.