The Tetrahymena thermophila genome sequence: 3. Completing macronuclear chromosome sequence scaffolds and ordering and aligning them along the micronuclear genome

Abstract

In Ciliates, the diploid, mitotic, genetically silent micronucleus (MIC) is the cell's germline, while the macronucleus (MAC) is the exclusive site of gene expression. During (postzygotic) MAC differentiation in T. thermophila, several hundred chromosomes are generated by site specific fragmentation of the five germline‐derived chromosomes at highly conserved chromosome breakage sites. Telomeres are added to every newly generated end, and chromosomes are amplified to ∼45 N. The Tetrahymena thermophila macronuclear genome was recently whole‐genome‐shotgun sequenced to nine‐fold redundancy at TIGR. The sequence (publicly available at http://www.tigr.org/tdb/e2k1/ttg/) is assembled into contigs (contiguous segments of overlapping sequence reads) linked into scaffolds. Here, we report here the completion of the assembly of many scaffold ends by linking them to their corresponding telomere, using diverse bioinformatic or experimental approaches. 120 chromosomes are now assembled from telomere to telomere and 125 additional scaffolds are telomere capped at one end. The 120 complete scaffolds encompass ∼45% of the ∼105‐Mb assembly, suggesting a total of ∼290 MAC chromosomes. By using paired sequence tags flanking chromosome breakage sites, we are linking unambiguously ordered and oriented MAC chromosome DNA sequence into MIC genome assemblies.Supported by NIH grant RR02931. Preliminary sequence data were obtained from The Institute for Genomic Research website.