Structure and sequence variation of the trypanosome spliced leader transcript

We have assessed the potential of using the spliced leader (SL) or mini-exo n gene as a marker for molecular phylogenetic analysis of genus Trypanosoma . A total of 27 trypanosome sequences were compared. 18 of these being newl y reported. In contrast to genus Leishmania, we found the non-transcribed s pacer region of the SL locus in trypanosomes to be far too variable for inf ormative comparison of all but the most closely related species. At the oth er extreme, the short (39 nt) SL tron was usually completely conserved and hence uninformative. The SL RNA showed variation in both length (97-152 at) and sequence among different trypanosome species, with most variation occu rring in stern-loop II. Consequently, this region could not be aligned with confidence in multiple sequence alignment, severely reducing the number of phylogenetically informative nucleotide positions. In computer simulation, most of the SL RNAs readily folded into the 3 stem-loop secondary structur e predicted previously, but again stem-loop II was highly variable. No obvi ous correlation could be seen between the length of this stem-loop and tryp anosome biology. We conclude that the SL repeat is not an informative phylo genetic marker for long range evolutionary studies of genus Trypanosoma. (C ) 2000 Elsevier Science B.V. All rights reserved.