Stylonychia lemnae macronuclear genome assembly. Stylonychia lemnae strain:130c

Like many ciliates, Stylonychia lemnae is typified by the presence of dimorphic nuclei: a small, germline micronucleus and a massive, vegetative macronucleus. Stylonychia’s macronuclear genome has a unique architecture, with highly amplified, gene-sized “nanochromosomes”. Here we report our analysis of the draft Stylonychia lemnae Mac genome assembly. Our best assembly is 50.2 Mb, has in excess of 16,000 complete nanochromosomes, and is assembled as less than 20,000 contigs. After extensive exploration of genome assemblers and assembly parameters, we found two successful assembly strategies: a custom assembly extension/meta-assembly pipeline (Terminator 2.0), and a genome assembler designed for assembling single-celled bacterial genomes (SPAdes). We were able to completely assemble the most highly amplified Stylonychia nanochromosome (7.5 kb), encoding the 18S, 5.8S and 28S rRNA, and the 65 kb Jotin nanochromosome orthologous to the longest nanochromosome in Oxytricha trifallax (a close relative of Stylonychia). We found considerable conservation of fundamental genomic properties between S. lemnae and O. trifallax, including nanochromosomal gene synteny and copy number. Protein domain searches and comparisons of the Stylonychia and Oxytricha predicted proteins revealed two new telomere binding proteins and the presence of linker histones. Among the diverse set of Stylonychia/Oxytricha histone variants, we found co-expressed, divergent histone variants corresponding to 4 of the 5 core nucleosomal proteins (H1.2, H2A.6, H2B.4 and H3.7) suggesting specialized nucleosomes may be involved in genome processing during nuclear differentiation.