The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses

Abstract

The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular biology. However, some investigations have been limited due to the incomplete closure and sequencing of the macronuclear genome assembly, which for many years has been stalled at 1,158 scaffolds, with large sections of unknown sequences (available in Tetrahymena Genome Database, TGD, http://ciliate.org/). Here we completed the first chromosome-level Tetrahymena macronuclear genome assembly, with approximately 300× long Single Molecule, Real-Time reads of the wild-type SB210 cells-the reference strain for the initial macronuclear genome sequencing project. All 181 chromosomes were capped with two telomeres and gaps were entirely closed. The completed genome shows significant improvements over the current assembly (TGD 2014) in both chromosome structure and sequence integrity. The majority of previously identified gene models shown in TGD were retained, with the addition of 36 new genes and 883 genes with modified gene models. The new genome and annotation were incorporated into TGD. This new genome allows for pursuit in some underexplored areas that were far more challenging previously; two of them, genome scrambling and chromosomal copy number, were investigated in this study. We expect that the completed macronuclear genome will facilitate many studies in Tetrahymena biology, as well as multiple lines of research in other eukaryotes.

SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping

“…Scrambled genes have been described in most hypotrich ciliates (Chang et al 2005;Hogan et al 2001), Chilodonella uncinata (Katz and Kovner 2010) and some Postciliodesmatophora ciliates (Maurer-Alcalá et al 2018). A recent report also validated the presence of scrambled loci in Tetrahymena (Sheng et al 2020), providing further evidence that this is common to ciliate genomes. By using split read mapping, we find that SIGAR can infer some scrambled chromosome architectures and their associated pointers, even in the absence of a MIC genome assembly.…”

“…After mating, a new MAC genome rearranges from a copy of the zygotic MIC, together with massive DNA elimination (Chen et al 2014;Hamilton et al 2016). The retained, macronucleardestined sequences (MDS) must be properly ordered and oriented, and sometimes even descrambled (Chen et al 2014;Sheng et al 2020), to form functional MAC chromosomes ( Figure 1A).…”

“…Thus, many high quality MAC genomes have been assembled using short next-generation sequencing reads. By taking advantage of third generation sequencing long reads, some MAC genomes have been assembled with unprecedented completeness (Wang et al 2020;Sheng et al 2020), sometimes obviating the need for assembly when the average read length exceeds the typical chromosome length (Lindblad et al 2019). In contrast, sequencing and assembling the long MIC genomes is experimentally and computationally complex.…”

SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping

“…The retained, macronuclear destined sequences (MDS) must be properly ordered and oriented, and sometimes even descrambled ( Chen et al. 2014 ; Sheng et al. 2020 ), to form functional MAC chromosomes ( fig.…”

“…Thus, many high-quality MAC genomes have been assembled using short next-generation sequencing reads. By taking advantage of third generation sequencing long reads, some MAC genomes have been assembled with unprecedented completeness ( Sheng et al. 2020 ; Wang et al.…”