Fig. 2.

Evolution of L1 s and SINEs in the pig genome. a Structural schematics of the putatively active L1 s and pig-specific SINE families (SINEA, SINEB, and SINEC). b Age distribution of pig-specific L1 families. c and d Age distribution across the subfamilies (L1D1–21) of the youngest L1 family (L1D). e Insertion polymorphism (IP) detection of the youngest L1 (L1D1) and SINE (SINEA1) subfamilies by PCR. Breed name abbreviations: Meishan (MS), Shawutou (SWT), and Jiangquhai (JQH) pigs are native Chinese pig breeds from Jiangsu Province; the Sujiang (SJ) pig is a newly established breed based on the Duroc and Jiangquhai bloodlines; Bama (BM) pigs are miniature pigs from Guangxi Province; the wild boar (WB) was from Anhui Province; and the Landrace (LD) and Yorkshire (YK) pigs were from a breeding farm in Anhui Province. Ne, negative control without DNA. Two transposon loci in each of the youngest transposon subfamilies were selected for insertion polymorphism (IP) detection and labeled as IP1 and IP2. If an individual contains SINE insertion at SINE-IP1 or SINE-IP2 site, the band size would be 629 or 676 bp, respectively, and if no SINE insertion, the band would be 335 or 382 bp. The three bands showed in the M (marker) lane are 750 bp, 500 bp and 250 bp from top to bottom. f) Age distribution of pig-specific SINE families. g and h Age distribution across the subfamilies (SINEA1–11) of the youngest SINE family (SINEA). The x-axis represents the insertion age (Million years ago, Mya), and the y-axis represents the percentage of the genome composed of retrotransposon families/subfamilies (%) in Fig. b, c, f, and g