Lateral Gene Transfer detected in Eukaryotic rRNA genes

This paper is an example of super cool science that also makes me worry. Eukaryote are known to have lower levels of Lateral Gene Transfer (LGT), and before this paper I assumed that LGT would not impact eukaryotic rRNA genes. However, this not so according to Yabuki et al. (2014):

Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genomewalking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two proteincoding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.

Why is this paper worrisome? Well, if LGT of rRNA genes is a widespread phenomenon in microbial eukaryotes, it will conflate biodiversity estimates obtained from environmental sequencing studies. If you had a environmental rRNA Illumina dataset, your bioinformatic analysis would show taxonomic assignments for an alveolate and stremenopile (detecting 2 taxa from one genome, one true assignment, one false). The authors cite this concern in their conclusion:

These large-scale [environmental] surveys may detect transferred rRNA genes and such transferred rRNA genes may confuse our understanding of the true diversity and distribution of microbial eukaryotes, even if the frequency of lateral transfers of the rRNA gene is rare and the copy numbers of the transferred rRNA gene in environments are low. We agree that environmental rRNA gene surveys with PCR are still useful and effective to estimate the diversity/ distribution of microbial eukaryotes. However, the fact that recovered rRNA gene sequences do not always reflect the actual existence of microbial eukaryotes corresponding to these sequences should be kept in mind based on our findings. 

In other words, more research is needed to determine exactly how widespread this rRNA LGT phenomenon is in eukaryotes...it may be something else we need to take into account when designing software workflows for environmental sequence data.

Reference:

Yabuki, A., Toyofuku, T., & Takishita, K. (2014). Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes, 1–4. doi:10.1038/ismej.2013.252