Arabidopsis thaliana nucleolar organizer region assembly using ultra-long Oxford Nanopore sequencing and dotplot puzzle fitting
About Anastasia McKinlay
Anastasia McKinlay is a Research Associate in Prof. Craig Pikaard’s Lab in the Department of Biology, Indiana University, and received her Ph.D. from Michigan State University with Prof. William Henry. During her post-graduate training with Prof. Stanley Fields in the Department of Genome Sciences, University of Washington, Anastasia applied next-generation sequencing to study nascent RNA transcription on a genome-wide scale. Currently, in Craig Pikaard’s Lab, she focuses on sequencing and assembly of the highly repetitive ribosomal RNA gene-containing loci.
Nucleolus organizer regions, or NORs, are chromosomal loci at which ribosomal RNA genes are repeated in long tandem arrays. In the Arabidopsis thaliana genome, two NORs are located at the distal ends of Chr2 and Chr4, span across megabase-long regions, and consist of hundreds of nearly identical in sequence rRNA genes, each ~10 kb in length. By applying a similarity matrix algorithm to ultra-long Oxford Nanopore reads, we were able to visualize patterns of subtle sequence variation within rRNA gene arrays that allow the overlapping reads to be merged to generate megabase-long assemblies of the Arabidopsis thaliana NORs.