Oxytricha trifallax strain:JRB310 Genome sequencing

Oxytricha trifallax is a ciliate, a binucleate protist that undergoes extensive programmed genome editing. During sexual development, the ~500 Mb germline genome, with approximately 70 diploid, megabase-scale chromosomes, rearranges into the ~50 Mb somatic genome, consisting of thousands of highly-polyploid, highly-genic nanochromosomes. While the coding content of the precursor germline genome is largely known, germline chromosomes had not previously been assembled. The 2014 germline assembly consists of >20,000 contigs, with an N50 >27 kb, and therefore it was unknown where developmentally retained fragments map in relation to one another from a genome-wide view, which is critical towards understanding the spatial and chromatin-level dynamics of rearrangement. Using HiC-based techniques to identify syntenic contigs from the previous fragmented assembly, and Nanopore long-read sequencing to fill in gaps, this assembly yields megabase-scale scaffolds of the Oxytricha germline genome. With massively improved contiguity, including two long scaffolds that contain two telomeres, this assembly allows for global mapping of the distribution of genomic features, and for the study of the 3D and epigenetic structure of the rearranging genome.