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Genome Biol Evol. 2014 Jun 20;6(7):1707-23. doi: 10.1093/gbe/evu139.

The draft assembly of the radically organized Stylonychia lemnae macronuclear genome.

Author information

  • 1Institute of Cell Biology, University of Bern, Switzerland.
  • 2Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, Germany.
  • 3Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, GermanyDepartment of Neonatology, HELIOS Children's Hospital, Witten/Herdecke University, Wuppertal, Germany.
  • 4Biology Department, Bradley University.
  • 5Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, Germany hans-joachim.lipps@uni-wh.de mariusz.nowacki@izb.unibe.ch estienne.swart@gmail.com.
  • 6Institute of Cell Biology, University of Bern, Switzerland hans-joachim.lipps@uni-wh.de mariusz.nowacki@izb.unibe.ch estienne.swart@gmail.com.

Abstract

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.

© The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

KEYWORDS:

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

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