Genome-wide in-silico identification and characterization of LTR retrotransposons in domestic goat (Capra hircus).

Abstract

This study employs LTR_Finder to identify and characterize mobile genetic elements, specifically long terminal repeat (LTR) retrotransposons, in the whole genome of domestic goats ( Capra hircus). LTR retrotransposons are a class of mobile genetic elements that replicate via an RNA intermediate and are flanked by long terminal repeat sequences. Previous studies have highlighted the complexity and significance of LTR retrotransposons in Capra hircus genome, particularly their role in genetic diversity, genome evolution, and potential functional implications. For the present analysis, the reference genome from NCBI was used, and the annotated results from LTR_Finder were further examined using Microsoft Excel, NCBI, Ensembl, Dfam, and Repbase. A total of 1741 L retrotransposons were identified, representing 23.27% of the complete Capra hircus genome. Among chromosomes, chromosome 23 contained the highest proportion of LTR retrotransposons. The longest LTR retrotransposon, measuring 22 kb, was detected on chromosome 28, and phylogenetic analysis confirmed its presence in other species within the Bovidae family. Conversely, the shortest LTR retrotransposon, with a length of only 1244 bp, was located on chromosome 1. Further classification revealed that 35% of the identified LTR retrotransposons were nested elements. In addition, they exhibited 177 distinct TSD sequences, along with conserved PBS (Primer Binding Site) and PPT (Polypurine Track) motifs, both of which are valuable for evolutionary analysis. Family-level classification using the UCSC Genome Browser identifies groups such as BTLTR, ERVL, ERVL_MaLR, ERVK, and Gypsy, thereby providing insights into the insertion patterns of LTR retrotransposons introduced by various retroviruses. Overall, these findings expand the understanding of the distribution, diversity, and evolutionary significance of LTR retrotransposons in the goat genome, underscoring their pivotal role in shaping genomic architecture and functional dynamics.