DNA nucleotide sequence analysis of the Pvull DNA fragment L of the genome of insect iridescent virus type 6 reveals a complex cluster of multiple tandem, overlapping, and interdigitated repetitive DNA elements

Abstract

The DNA nucleotide sequence of the Pvull DNA fragment L (0.920 to 0.944 map units (m.u.)) of the genome (209 kbp) of insect iridescent virus type 6 was determined. The size of this DNA fragment was 5064 by with a base composition of 39.79% G + C and 60.21 % A + T. The DNA sequence contained many perfect direct repeats of sizes up to 145 bp. In addition to these repetitions, a cluster of four imperfect repetitive DNA elements (R1 to R4) with a complex structural arrangement was detected. R1, R2, and R3 existed in duplicate (two ☐es (B)) between nucleotide positions 271 and 3466) and their size were as follows: R1-B1/B2 (567/568 bp), R2-B1/B2 (917/931 bp), and R3-B1/B2 (92/88 bp). The R4 repetitive element was found in 12 ☐es (between bases 1301 and 4417), which were interrupted at nucleotide positions 1883 to 2236 and 3341 to 3587. These interruptions define three segments (S) harboring ☐es 131 to B3 (S1), B4 to B8 (S2), and B9 to B12 (S3). The size of the individual ☐es was found to be 239, 233, 107, 244, 222, 242, 242, 148, 240, 242, 242, and 102 by for R4-B1 to B12, respectively. Five open reading frames (ORFs of 118 to 333 amino acid (AA) residues) were detected. The analysis of the amino acid sequences of the largest ORF revealed that the deduced amino acid sequence of the putative gene product contained two repetitions TR1 (three domains of 50 AA) and TR2 (two domains of 74 AA). Sequences of 43 amino acid residues of ORF 5 (160 to 202 AA) were homologous within the majority of ORFs. A consensus sequence-MAN L(X) 6 IGSSST(X) 6 L(X) 1 LGS(X) 1 LQISG(X) 2 L(X) 1 VN-was found in all five ORFs. Although classical canonical and noncanonical transcriptional start signals were detectable, polyadenylation signals were not observed.