In addition, approximately 30% of the A. carolinensis genome consists of repetitive mobile element sequences, which leads to a lower than typical N50 given the sequencing depth.
The assembly alleles that show substantial similarity with simple repeats or mobile element sequences in RepBase are annotated as variable number of tandem repeats (VNTR) or transposable element insertion (TEI), respectively.
These studies identified a variety of genetic mechanisms involved in creating new genes, including gene duplication, gene fusion and fission, exon shuffling, recruitment of new exons from mobile element sequences, retroposition, lateral gene transfer, and de novo origination (i.e., from previously noncoding sequence).
Mobile genetic element sequence data consisted of MGEs from the Phast [ 49] and the ACLAME databases [ 50].
One hundred and ninety-five out of a total of 19 751 clusters, corresponding to the most abundant families of genomic repeats, were analysed for their similarity to known sequences using RepeatMasker Open-3.0 (http://www.repeatmasker.org) and BLAST (Altschul et al., 1990) searches against GenBank databases and a database of plant mobile element protein sequences (Novák et al., 2013).
Most relationships are resolved and strongly supported by mobile elements and sequence data.
Overall, our study provides the most comprehensive view on colobine evolution to date and emphasizes that analyses of various molecular markers, such as mobile elements and sequence data from multiple loci, are crucial to better understand evolutionary relationships and to trace hybridization events.
The simplest mobile element, the insertion sequence (IS), encompasses only a transposase enzyme and a pair of short inverted repeat sequences that flank the transposase gene and function as recognition sites where the DNA breaking joining reactions occur.
Our intra-repeat element PCR assays were designed to facilitate effective amplification of both gibbon and human elements, while also preventing cross-amplification with any other type of mobile element or genomic sequence.
Mobile elements (insertion sequences and miniature inverted repeat transposable elements) have been mapped to the chromosome to identify disrupted genes (40).
