Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

Abstract

Interspersed repeat composition and distribution in mammals have been best characterized in the human and mouse genomes. The bovine genome contains typical eutherian mammal repeats, but also has a significant number of long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata. Our analysis of the BovB repeats has indicated that only a few of them are currently likely to retrotranspose in cattle. However, bovine L1 repeats (L1 BT) have many likely active copies. Comparison of substitution rates for BovB and L1 BT indicates that L1 BT is a younger repeat family than BovB. In contrast to mouse and human, L1 occurrence is not negatively correlated with G؉C content. However, BovB, Bov A2, ART2A, and Bov-tA are negatively correlated with G؉C, although Bov-tAs correlation is weaker. Also, by performing genome wide correlation analysis of interspersed and simple sequence repeats, we have identified genome territories by repeat content that appear to define ancestral vs. ruminant-specific genomic regions. These ancestral regions, enriched with L2 and MIR repeats, are largely conserved between bovine and human.cow ͉ BovB ͉ microsatellite ͉ repetitive DNA

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

“…3 and Supplementary Table 6). However, the goat genome has ~80% fewer SINE-BovA repeats (971,273 in goat and 1,839,497 in cattle) and >40% more SINE-tRNA repeats (665,366 in goat and 388,920 in cattle) than does the cattle genome, suggesting that the SINE-BovA repeat expanded primarily in the cattle genome 22 , whereas the SINE-tRNA repeat expanded specifically in the goat. We also analyzed the degree of divergence for each type of transposable element in the goat genome, and found few recently diverged transposable element classes (Supplementary Fig.…”

“…Transposable elements make up a substantial fraction of mammalian genomes and contribute to gene and/or genome evolution 22 . The goat genome has transposable elements similar to those of cattle 22 in that the genome contains large numbers of ruminant-specific repeats, which comprise 42.2% of the goat genome ( Fig.…”

“…The goat genome has transposable elements similar to those of cattle 22 in that the genome contains large numbers of ruminant-specific repeats, which comprise 42.2% of the goat genome ( Fig. 3 and Supplementary Table 6).…”

Identification of simple sequence repeat markers in the dromedary(Camelus dromedarius) genome by next-generation sequencing

“…This is because the development of SSR markers is labor-intensive and requires library construction and screening (17). Most recently, high throughput of next-generation sequencing (NGS) enabled the development of genome-wide SSR markers such as alpaca transcriptome (19) and bovine genome (20). The goal of the present study was to identify SSR markers from the dromedary (Camelus dromedarius) genome and investigate their polymorphic nature for genetic applications by using camel breeds bred in Saudi Arabia.…”

Repeats as global DNA methylation marker in bovine preimplantation embryos

“…Besides satellite DNA, most of the DNA methylation in mammalian genomes is found in retrotransposons (Schulz et al 2006). Retrotransposons, which account for almost half of the genome (44% of bovine genome (Adelson et al 2009) and 45% of human genome (Lander et al 2001)), were previously suggested as biomarker for global methylation status (Klose and Bird 2006). Recent research on epigenetics of mammalian preimplantation embryos found that transposable elements show a similar dynamic trend towards global methylation (Guo et al 2014).…”