Genome structure and characterisation of an endogenous retrovirus from the zebrafish genome project database

Abstract

A 9.5Kb nucleotide sequence of an endogenous retrovirus was obtained during an attempt to screen a reverse transcriptase-like element in the zebrafish genome project database. The element termed here as ZFERV-2 has the typical genomic organization of a retrovirus in which the LTR flanks the viral genes in this way: LTR-gag-pol-env-LTR. ZFERV-2, resembles a zebrafish endogenous retrovirus, ZFERV discovered previously by Shen and Steiner (2004) and has all the major conserved motifs of the viral genes. In addition, ZFERV-2 has several characteristics possessed by a retrovirus. Firstly, ZFERV-2 shows a replication defective retrovirus because of huge deletion at the protease gene proximal to gag gene is observed. Secondly, an intact genome structure of ZFERV-2 together with 99% sequence similarity on both ends of the LTRs indicate a recent integration into the zebrafish genome. Thirdly, a long leader sequence at 1.5Kb upstream of the viral genes and a large genome size are characteristics shared by retroviruses isolated from lower vertebrates. © Springer-Verlag Berlin Heidelberg 2008.