Genome wise identification of long terminal repeats in Bubalus bubalis

Abstract

Bovines are important livestock species contributing towards food (milk and meat), draft power and fuel. Buffalo is important for Indian subcontinent and far East countries of Asia and Brazil. Striking difference between the cattle and buffalo is attributed to distinct novelties between them at genomic level. Long terminal repeat (LTR) retrotransposons make up a large fraction of the typical mammalian genome. The abundance of LTR retro-transposons are believed to hold major significance for genome structure and function. The present study is an effort to identify the contribution of LTR to Bubalus bubalis genome, their abundance and the distribution of LTRs was examined in the buffalo genome version Bbu_2.0–alpha using web based algorithm. The buffalo chromosomes were screened against tRNA database of Bos taurus. A total of 26,338 LTRs were observed from the buffalo genome. Chromosome 1 exhibited the maximum number of LTRs i.e. 2232 and the minimum i.e. 324 LTRs were observed in chromosome 24. It was observed that more LTRs were present on sense strand than on antisense strand. 11 LTR regions were found to be coding for the Reverse Transcriptase (RT). Target site repeats (TSR) were AT rich. The density of the LTR along the length of chromosomes revealed that the LTR are present abundantly in the middle of autosomes than at the end except chromosome X. Being source of genetic variability and having evolutionary significance, an indepth analysis of LTRs may provide a clue for the significant difference between cattle and buffalo genomes.