Comment on "PstI repeat, a family of short interspersed nucleotide element (SINE)-like sequences in the genomes of cattle, goat, and buffalo"

Lenstra Nijman 175 Digestion of genomic DNA from cattle, sheep or goat by PstI produces a discrete band of about 500 bp, a restriction fragment of the Bov-B short interspersed nuclear element (SINE) (Duncan 1987; Majewska et al. 1988; Lenstra et al. 1993; Szemraj et al. 1995). Bov-B is shared by all ruminants and Bov-B insertions have occurred early on, as well as later, during the evolution of this suborder (Jobse et al. 1995; Nijman et al. 2002). Sheikh et al. (2002) have cloned, sequenced, and compared repetitive PstI fragments from the genomes of cattle, goat, and water buffalo. The 489-bp bovine fragment is similar to Bov-B and is designated as a type I PstI repeat. Surprisingly, an alignment (Fig. 4 from Sheikh et al. 2002) shows that a type II PstI repeat from goat and buffalo with the about same length is not similar to the bovine element (about 48% identity). Further, it is suggested that the goat and buffalo elements have evolved separately, whereas a BLAST search revealed a significant similarity of the goat repeat to bovine serine tRNA. However, an alignment of the same sequences (Appendix 1) as listed in Fig. 4 of Sheikh et al. (2002) shows that in fact Bov-B, represented by the database entry btrppst1, is similar to both the bovine type I sequence (77% identity) and the complementary strands of the goat and buffalo type II sequences (77 and 76% identity, respectively). Therefore, the separate positions of the type I and type II sequences in a phylogenetic tree (Fig. 5 of Sheikh et al. 2002) reflect the difference between complementary strands and there is no evidence for a separate evolution of the PstI repeats. Similarity of SINEs from several different species including the ruminant Bov-tA SINE to tRNA sequences has been observed repeatedly (Ogiwara et al. 2002). However, the BLAST match of the goat type II repeat to the bovine serine tRNA gene appears to be due to the presence of a Bov-B repeat element 636–240 bp upstream of the tRNA sequence, and ot because of any resemblance between the goat PstI repeat and the tRNA itself. In line with previous (Jobse et al. 1995) and more recent (Nijman et al. 2002) data, we conclude that the genomes of cattle, goat, and buffalo contain the same type of PstI SINE repeats, which is not derived from a tRNA sequence.

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