Fig. 1: TE annotation and SINE classification in the pig genome.
From: Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits
a A schematic of the Pig Transposable Element Detection and Classification (PigTEDC) pipeline. It is composed of three TE detection approaches, which use similarity-, structure-, and de novo-based algorithms. b The proportion of TEs from different superfamilies in the count. c The proportion of TEs from different superfamilies in length. d Classification of pig TE superfamilies and families (ā„3000 copies in each family). e Sequence divergence distribution for TE superfamilies (upper panel) and families (bottom panel) in the pig genome. Sequence divergence distributions are plotted in bins of 0.01 increments. f Phylogenetic tree and sequence divergence distribution for SINE families in the pig genome. On the right panel, the x-axis represents the divergence, and the y-axis represents the counts of the SINE families. g Boxplots display the proportion of genomic SVs formed by different SINE families. h Boxplots display the proportion of genomic SVs formed by different SINE subfamilies. See Supplementary DataĀ 1 for their definitions. i Classification of pig SINE families based on their ages. The line inside each boxplot represents the median.
