1 Comparative genomics of Oxytricha and related spirotrichous ciliates: Minimal eukaryotic genome architectures

To augment the study of the extremely fragmented genomes of spirotrichous ciliates and to improve our understanding and annotation of the Oxytricha trifallax strain JRB310 genome, we propose the sequencing of a set of additional genomes, to various depths. This work would be based on the already supported and ongoing sequencing of the 50 Mb Oxytricha trifallax JRB310 macronuclear and (~50 Mb sample of the 1Gb) micronuclear genome, being performed at the Washington University Genome Sequencing Center (PI Elaine Mardis). We suggest (1) as a complement to the current sequencing of O. trifallax, deeper coverage of its 1 Gb germline micronuclear genome, to a full 2X coverage, rather than the mere 50 Mb of sequence that was originally approved as a companion to the O. trifallax macronuclear genome in March 2002 (5 years ago). At least this level of resolution will be required to permit reasonable accuracy in assigning scrambled gene segments from the micronucleus to a subset of genes from the macronucleus and allow us to study the general cellular and evolutionary mechanism of its global DNA rearrangements. (2) We request high quality draft sequence of the macronuclear genome of Stylonychia lemnae. S. lemnae is one of the most studied ciliates, and its evolutionary distance from O. trifallax is appropriate for efficient phylogenetic footprinting (see below for details). A comparative study between S. lemnae and O. trifallax genomes would lead to a better deciphering of both genomes in a synergystic manner, and lead to a better understanding of the genome unscrambling and DNA eliminatio