Intra-Genomic Variation in the Ribosomal Repeats of Nematodes

Happy to announce our new paper, published last week in PLoS ONE:

Bik HM, Fournier D, Sung W, Bergeron RD, Thomas WK (2013) Intra-Genomic Variation in the Ribosomal Repeats of Nematodes. PLoS ONE 8(10): e78230. doi:10.1371/journal.pone.0078230

This manuscript was in the works for a while, and was based on undergraduate research carried out by co-author Dave Fournier while he was an undergraduate at UNH. The rationale? To assess the level of variation in rRNA loci within a single nematode genome, as well as between genomes of different nematode species. rRNA is typically present as a repeated, muti-copy locus in eukaryote genomes, which makes it hard (impossible) to correlate gene abundance to organismal abundance in environmental sequencing studies. Unlike bacteria, there is no known correction that we can apply to "normalize" DNA for species with multiple rRNA copies - every species has multiple copies (sometimes into the thousands!) and we know little about the typical ranges of rRNA copy number across different eukaryote groups.

In this manuscript were were asking questions about both rRNA copy number (how many rRNA repeats are present in a genome?) and intragenomic variation (how many of these copies are unique rRNA gene sequences within a genome, and across rRNA variants are there "hotspots" for base polymorphisms?). We wanted to determine if we could spot patterns that govern rRNA copy number and level of intragenomic variation amongst gene copies - taking into account things like genome size and phylogenetic distance.

The result? There doesn't seem to be any pattern determining copy number or intragenomic rRNA variants across species, which kind of makes biodiversity estimates from environmental rRNA studies feel like a shot in the dark. But we DID find some interesting evidence of selection acting on rRNA loci:

By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function.

Divergence and polymorpishm are illustrated in the figure below:

Figure 1. Variation observed in nematode ribosomal arrays. (A) Divergence in rRNA repeats observed between the genomes of C. elegans, C. briggsae, C. japonica, and C. remanei; here, base substitutions are denoted as transitions or transversions, while complex polymorphisms represent any type of insertion, deletion, or inversion event. (B) Polymorphic positions in rRNA repeats observed within the genomes of each Caenorhabditis species. Results suggest that the pattern of intragenomic polymorphisms is unique across repeats within a species, whereas patterns of interspecific divergence reflect a strong signature of natural selection for rRNA function. 

The data on genomic patterns in eukaryotic rRNA is still very preliminary, and this paper is just a starting point. Hopefully this type of work will inspire similar analyses in other groups - we desperately need more knowledge, particularly for non-model organisms.