Is it a Mammal Thing? Determining When the Change in rDNA Unit Size Occurred in Amniotes

Emma Macdonald0, Austen Ganley0, Richard Edwards1
(0) The University of Auckland
(1) The University of New South Wales

Find me on Wed Nov 25th, 1:30-2:50pm AEDT in Remo, table 86

Abstract
The ribosomal RNA genes in eukaryotes are organised into long arrays of tandem repeats, collectively termed ribosomal DNA (rDNA). Each rDNA repeat unit comprises a rRNA coding region and an intergenic spacer. Eukaryotes exhibit remarkably little variation in rDNA unit size, with the majority ranging between 9 - 15 kb in length. Mammals, though, present a striking exception to this rule, with rDNA unit sizes of ~45 kb. However, rDNA unit size is poorly characterized in amniotes, of which mammals are a member, partly due to the repetitive nature of the rDNA limiting short-read assemblies of this region. Thus, it is unclear where in amniote evolution this rDNA unit size increase occurred, or why. Here, we utilised Oxford Nanopore datasets to determine if long rDNA unit sizes are limited to mammals or are widespread among members of the amniote clade. We used BLAST to identify reads with at least two rDNA units and calculated their size through the average distance between rDNA units. Analysing over 100 reads per species revealed that the bird, snake, lizard, and turtle lineages, as well as the tuatara, all have short rDNA unit sizes. In contrast, we show that marsupials have a long rDNA unit size. These results demonstrate that expansion of the rDNA unit size occurred after the divergence of mammals and marsupials from the amniotes. We are now attempting to obtain monotreme long-read datasets to determine whether this increase in rDNA unit size occurred before or after monotremes split from the remaining mammalian lineages. Our results illustrate the value of long-read sequencing for investigating regions of the genome that are typically refractory to analysis. Pinpointing where in amniote evolution the rDNA size underwent a dramatic increase will allow us to then ask how and why this increase might have occurred.