Plant species mapping

Tetrahymena thermophila is a free-living protozoan, common in fresh water. A popular model organism, it is the best-studied of the ciliates - a diversified and successful lineage of eukaryotic protists.

Mirroring the way in which higher eukaryotes have distinct germline and somatic cells, so the single-celled Tetrahymena partitions its genome into two nuclei. The smaller micronucleus acts as the germline: it contains a diploid set of chromosomes, undergoes meiosis and fertilization, and determines the genotype of the offspring, but is transcriptionally inert. The larger macronucleus, in contrast, contains about 50 copies of the genome in the form of small chromosomes derived from the micronuclear chromosomes by a controlled process of fragmentation; these act as the transcriptionally active "working copies" of the genome.

The ~100Mb macronuclear genome has recently been shotgun sequenced by TIGR, and the genome paper appeared in PLoS Biology in August 2006. In collaboration with Eduardo Orias' group at UCSB, we are using HAPPY mapping to guide the assembly of the shotgun scaffolds to reconstruct all of the ~250 macronuclear chromosomes. The complete macronuclear assembly will, in turn, act as a stepping-stone to allow us to reconstruct the larger chromosomes of micronuclear genome.


	Tetrahymena thermophila Tetrahymena thermophila is a free-living protozoan, common in fresh water. A popular model organism, it is the best-studied of the ciliates - a diversified and successful lineage of eukaryotic protists. Mirroring the way in which higher eukaryotes have distinct germline and somatic cells, so the single-celled Tetrahymena partitions its genome into two nuclei. The smaller micronucleus acts as the germline: it contains a diploid set of chromosomes, undergoes meiosis and fertilization, and determines the genotype of the offspring, but is transcriptionally inert. The larger macronucleus, in contrast, contains about 50 copies of the genome in the form of small chromosomes derived from the micronuclear chromosomes by a controlled process of fragmentation; these act as the transcriptionally active "working copies" of the genome. The ~100Mb macronuclear genome has recently been shotgun sequenced by TIGR, and the genome paper appeared in PLoS Biology in August 2006. In collaboration with Eduardo Orias' group at UCSB, we are using HAPPY mapping to guide the assembly of the shotgun scaffolds to reconstruct all of the ~250 macronuclear chromosomes. The complete macronuclear assembly will, in turn, act as a stepping-stone to allow us to reconstruct the larger chromosomes of micronuclear genome.