The Tetrahymena thermophila genome sequence: 1. Genome-wide uniformity of macronuclear chromosome copy number in spite of amitotic (random) copy distribution

In Ciliates, the diploid, mitotic, genetically silent micronucleus is the cell's germline, while the macronucleus is the exclusive site of gene expression. Pre-genomic studies in Tetrahymena thermophila have shown that • The macronucleus contains 250–300 chromosomes, derived from the five germline chromosomes; • G2 copies of each chromosome are distributed amitotically (randomly) during macronuclear division. In heterozygotes, this results in the segregation of vegetative descendants expressing only one of the two alleles (assortment). Phenotypic assortment rate measurements for a handful of loci suggested a uniform macronuclear chromosome G1 copy number (∼45 per macronucleus; rDNA minichromosome excepted). The NIGMS/NSF-supported, whole-genome-shotgun sequencing of the T. thermophila macronuclear genome was recently completed at TIGR. (Sequence and scaffold databases, and related resources, are publicly available for blasting or downloading without restriction at http://www.tigr.org/tdb/e2k1/ttg/). Analysis of the depth of sequence coverage shows that (rDNA excepted) at least 95%—and possibly all—of the macronuclear genome is in chromosomes with uniform copy number. This implies the existence of regulatory mechanisms that independently correct the number of copies of nearly 300 different chromosomes after random distribution at every cell cycle. Supported by NIH grant RR02931. Preliminary sequence data were obtained from The Institute for Genomic Research website.