Chromosomal distribution, gene duplication, synteny analysis,
expression profiles and copy number variation
The chromosome distribution of PIM1 and adjacent genes were obtained
from the genome annotation information and visualized by TBtools
v1.098685 (Chen et al., 2020). Gene duplication events were identified
manually. Segmental duplication events were characterized as copying the
whole blocks of genes from one chromosome to another while tandem
duplication was defined as paralogous genes located within 50kb in
tandem and was separated by fewer than five nonhomologous spacer genes
(Cannon et al., 2004). The collinear blocks were detected by JCVI v0.7.5
(Tang et al., 2008) and visualized by Circos v0.69.8 (Krzywinski et al.,
2009).
Duplication of PIM gene were explored in other avian species. ThePIM gene family were identified in 47 avian genomes released by
Ensembl covered 12 avian orders (Accipitriformes, Anseriformes,
Apterygiformes, Casuariiformes, Charadriiformes, Falconiformes,
Galliformes, Passeriformes, Psittaciformes, Strigiformes,
Struthioniformes, Tinamiformes) by using the same method as the
identification of PIM in tree sparrow. Then according to the
completeness of pkinase domain, the identified PIM genes in all
avian species were divided into two categories: complete and incomplete.
The expression patterns of the chicken and tree sparrow PIM1 in
eight tissues (brain, heart, kidney, liver, lung, muscle, spleen,
testis) were analyzed following the method described in transcriptome
analysis. Except for the liver, spleen and testis of tree sparrow were
sequenced in our study, the other transcriptome data were downloaded
from NCBI sequence read archive (SRA) database. The expression heatmap
was generated by ComplexHeatmap v2.10.0 (Gu et al., 2016) package in R.
The expression level and copy number of the tree sparrow PIM1between LJX and BY were compared. We calculated the read depth perPIM1 gene and per individual by using bedtools v2.30.0 (Quinlan
& Hall, 2010). The read depth was normalized according the gene length
and the total reads aligned to the assembly genome per sample. Large
changes in read depth might indicate copy number variation between two
population.