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frozen since their early divergence from other eukaryotes (Gunzl et al., 2007). However, this interpretation is flawed for several reasons, particularly because there is no evidence whatsoever for an ancient divergence of kinetoplastids (Keeling et al., 2005). Nonetheless, the independent origin of the same features in dinoflagellates raises an intriguing alternative explanation, namely that the evolutionary origins of polycistronic mRNAs and trans-splicing are linked. This is all the more compelling when one considers that both features are also found together in the nematode Caenorhabditis elegans (Graber et al., 2007). It is unlikely that this is either functionally advantageous or an evolutionary relict, but rather that the evolution of one feature preconditions the genome by removing deleterious effects of the second feature. For example, the establishment of widespread SL addition in a nuclear genome could precondition that genome for the subsequent establishment of polycistronic transcription. Polycistronic mRNAs that would otherwise be deleterious could flourish simply because the processing pathway eliminates their deleterious effect (the inability to translate all but the first cistron). SL addition appears to be universal in both dinoflagellates and kinetoplastids [in C. elegans 70% of mature mRNAs are produced through trans-splicing: Graber et al. (2007)]. Polycistronic messages, however, are also near universal in kinetoplastids, whereas in dinoflagellates (and C. elegans) only a subset of genes are expressed on polycistonic mRNAs (Bachvaroff and Place, 2008). Since so far only tandem duplications of closely related copies of the same gene are known in dinoflagellates, it would appear they may arise and dissolve continuously.

The functional impacts of SL addition and polycistronic transcription are also different in the 2 lineages. Posttranslational control may be somewhat restricted by the absence of sequence diversity at the 5′ end of mRNAs, but more importantly a heavy use of polycistronic messages eliminates the possibility of transcription-level differentiation of expression of any genes within the same cluster. In kinetoplastids, there is only a handful of promoters and a marked paucity of transcription factors (Gunzl et al., 2007), unavoidably leading to the general lack of control over transcription initiation. Indeed, in the well-studied T. brucei, virtually all nuclear DNA seems to be permanently transcribed. Consequently, control levels in kinetoplastids are confined to RNA processing, export, and half-life, as well as translation and protein stability (Clayton, 2002). This is a good illustration of how convergent processes differ in the details in different lineages. In this case, the kinetoplastids cotranscribe many different genes whereas dinoflagellates cotranscribe many copies of the same gene, and as a result, transcription-level control is likely not so severely affected in the latter group.

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