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.
Highlights
As is characteristic of ciliates, Stylonychia lemnae possesses both a macronucleus (MAC), specialized for gene expression, and a micronucleus (MIC), containing the germline genome that permits recombination and transmission of genetic information across sexual generations (Prescott 1994)
The reduced fraction of matching telomeric reads may indicate that we have missed a small fraction of alternative nanochromosome ends, but as nanochromosome ends were typically found in nongenic regions in Oxytricha (Swart et al 2013) and only approximately 2% of all the reads do not map to the Stylonychia MAC genome assembly, we expect only a minor loss of sequence information
No genome assemblers are designed to cater to the unique properties of the highly fragmented stichotrich macronuclear genomes, that is, high levels of heterozygosity, nanochromosome copy number variation, alternative nanochromosome fragmentation, and variability of the telomere addition site
Summary
As is characteristic of ciliates, Stylonychia lemnae possesses both a macronucleus (MAC), specialized for gene expression, and a micronucleus (MIC), containing the germline genome that permits recombination and transmission of genetic information across sexual generations (Prescott 1994) (fig. 1). As is characteristic of ciliates, Stylonychia lemnae possesses both a macronucleus (MAC), specialized for gene expression, and a micronucleus (MIC), containing the germline genome that permits recombination and transmission of genetic information across sexual generations (Prescott 1994) Stylonychia has long and rich history as a subject for studies of nuclear organization and development, chromosomes and chromatin, and telomere biology and genome rearrangement (reviewed in Prescott 1994, 2000; Fuhrmann et al 2013). The MAC genomes of stichotrichous ciliates (including S. lemnae and Oxytricha trifallax) are organized as tiny, mostly gene-sized molecules with a minimal amount of subtelomeric noncoding sequence, allowing them to be exploited as natural gene finders for both protein-coding and noncoding RNA genes (Jung et al 2011; Swart et al 2013).
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