The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome.

Aeschlimann, Samuel H.; Jönsson, Franziska; Postberg, Jan; Stover, Nicholas A.; Petera, Robert L.; Lipps, Hans-Joachim; Nowacki, Mariusz; Swart, Estienne Carl (2014). The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome. Genome biology and evolution, 6(7), pp. 1707-1723. Oxford University Press 10.1093/gbe/evu139

Genome Biol Evol-2014-Aeschlimann-1707-23.pdf - Published Version
Available under License Creative Commons: Attribution (CC-BY).

Download (1MB) | Preview

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 variably and highly amplified "nanochromosomes," each usually encoding a single gene with a minimal amount of surrounding noncoding DNA. As only a tiny fraction of the Stylonychia genes has been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2-Mb draft S. 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 S. 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 protein homologs and the presence of linker histones. Among the diverse histone variants of S. lemnae and O. trifallax, we found divergent, coexpressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4, and H3.7) suggesting that these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the S. 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 S. lemnae macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Biology > Institute of Cell Biology > Ciliate
08 Faculty of Science > Department of Biology > Institute of Cell Biology

UniBE Contributor:

Nowacki, Mariusz, Swart, Estienne Carl


500 Science > 570 Life sciences; biology




Oxford University Press


[4] Swiss National Science Foundation ; [18] European Research Council


[UNSPECIFIED] Stylonychia lemnae genome project




Mariusz Nowacki

Date Deposited:

01 Sep 2014 15:01

Last Modified:

05 Dec 2022 14:36

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

macronuclear genome, nanochromosome, genome rearrangement, histone variant, chromosome copy number, alternative fragmentation




Actions (login required)

Edit item Edit item
Provide Feedback