A preliminary analysis of repetitive sequence organisation in <i>Bubalus bubalis</i> genome

Abstract

The most prevalent feature of eukaryotic genomes is their repetitive DNA sequences, which plays a critical role in genome evolution. Hence, identification and analysis of repetitive DNA regions are vital to understand genome structure and function completely. The investigation of repeats in preliminary draft sample of buffalo<i style=""> </i>genome with 60,999 contigs was carried out through comparison of sequences with those in curated repeat libraries using WU-Blast. It was found that around 80% of the genome can be currently recognized as repetitive elements including simple repeats, satellite, long terminal repeats (LTR) retrotransposons, long interspersed nuclear elements (LINE) and short interspersed nuclear elements (SINE), which together cover the total repetitive fraction. Repeat analysis revealed the presence of ribosomal RNA (rRNA) and transfer RNA (tRNA) repeats along with other repeats like DNA/hAT, DNA/TCMAR and a small amount of unknown repeats. A comparative analysis of repeats of the buffalo, cow, mouse and human genomes was also discussed.