The draft assembly of the radically organized Stylonychia lemnae macronuclear genome

Background Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: a small, germline micronucleus and a massive, vegetative macronucleus. The genome within Stylonychia’s macronucleus has a very unusual architecture, comprised of variably and highly amplified “nanochromosomes”, each usually encoding a single gene with a minimal amount of surrounding non-coding DNA. Since only a tiny fraction of the Stylonychia genes have been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2 Mb draft Stylonychia lemnae macronuclear genome assembly, containing in excess of 16,000 complete nanochromosomes, assembled as less than 20,000 contigs. We found considerable conservation of fundamental genomic properties between Stylonychia lemnae and its close relative, Oxytricha trifallax, including nanochromosomal gene synteny, alternative fragmentation and copy number. Protein domain searches in Stylonychia revealed two new telomere binding proteins and the presence of linker histones. Among the diverse histone variants of Stylonychia and Oxytricha, we found divergent, co-expressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4 and H3.7) suggesting these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the Stylonychia lemnae macronuclear genome demonstrates that largely complete, well-assembled highly fragmented genomes of similar size and complexity may be produced from one library and lane of Illumina HiSeq 2000 shotgun sequencing. The provision of the Stylonychia macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements.