Genomic resources already available or funded in Tetrahymena

Genetic maps. Germline linkage maps and macronuclear coassortment maps have been constructed based on ~400 DNA polymorphisms and linking an estimated 2/3 of the genome [1; 2; http://www.lifesci.ucsb.edu/~genome/Tetrahymena]. In addition, more than 100 partial deletions of germline chromosomes have been mapped [Cassidy-Hanley et al., unpubl. obs.].

Physical maps. Micronuclear sequence reads flanking an estimated 15% of the chromosome breakage sites (Cbs) have been obtained and they have all been assigned to MIC chromosome arms. The physical size of the two MAC chromosomes pairs flanking each of those Cbs has also been determined [3]. Funding is available to characterize the rest of the Cbs (estimated at ~ 300 total) This sequence data will eventually coassemble with MAC genome sequence and will allow determination of the order and orientation of MAC chromosomes in the germline genome.

About a third of the Cbs junctions have DNA polymorphisms, which have been mapped to linkage groups. In addition, more than 60 genetically mapped RAPD polymorphisms located on distinct MAC chromosomes have been sequenced and the size of the MAC chromosome has been determined. Another ~60 are being done (Orias lab). This work will anchor physical and sequence maps to the genetic map and facilitate the long-range assembly of genomic sequence. Funding is also available to the Orias lab to physically map, over the next three years, at least 2,000 sequenced-tagged sites (mainly ESTs), which will ultimately anchor the sequence map to the physical map of the genome.

The availability of anchored genetic, physical and sequence maps will not only facilitate the overall assembly of the genome sequence, but should also facilitate positional cloning of mutant genes whose phenotype does not provide selective growth advantage in either direction.

Proteins and ESTs. More than 150 experimentally characterized and annotated genes from T. thermophila (mainly) and T. pyriformis have been deposited in GenBank -- some are genomic, others are mRNA sequences. About 9,000 ESTs, derived from full-length cDNA library from exponentially growing cells [4], have been sequenced and submitted to GenBank [5; http://www.cbr.nrc.ca/reith/tetra/tetra.html]. Funding is also available to sequence an additional 20-40,000 ESTs from several libraries, mainly through a subproject, under Prof. Ron Pearlman's direction, of the Protist EST Project of the Atlantic Division of Genome Canada. The ESTs will be useful, not only for gene discovery, but also for training Tetrahymena gene finding programs.

References

1. Wickert S & Orias E (2000) Tetrahymena micronuclear genome mapping: A high-resolution map of chromosome 1L. Genetics, 154:1141-53.

2. Wickert S, Nangle L, Shevel S & Orias E (2000) Tetrahymena macronuclear genome mapping: colinearity of macronuclear coassortment groups and the micronuclear map on chromosome 1l. Genetics, 154:1155-67.

3. Hamilton EP, Bisharyan Y, Bruns P, Fridman V, Gerber J, Lin C, Merriam V, Orias E, Vong L & Cassidy-Hanley D (2002) Physical and genetic mapping of chromosome breakage junctions in Tetrahymena thermophila. Genetics, pending revision.

4. Chilcoat ND, Elde NC & Turkewitz AP (2001) An antisense approach to phenotype-based gene cloning in Tetrahymena. Proceedings of the National Academy of Sciences of the United States of America, 98:8709-13.

5. Fillingham, J., N. Chilcoat, A. Turkewitz, E. Orias, M. Reith, and R. Pearlman, Analysis of expressed sequence tags (ESTs) in the ciliated protozoan Tetrahymena thermophila. J. Euk. Microbiol., 2002. In press.