Lee H. Pratt

In part to address specific questions concerning genome evolution and function and in part to develop expertise in genome sequencing, Mrs. Aynsley Eastman has been sequencing three BACs from rice chromosome 3. Rice contains three genes encoding phytochrome apoproteins: PHYA, PHYB, and PHYC, which encode the apoproteins of phyA, phyB and phyC, respectively. Each of the three BACs contains a different phy. Sequences for two of the BACs have been completed, annotated, and deposited in GenBank: AF377946 and AF377947.

Among the specific questions to be addressed by Mrs. Eastman are the following.

1 - What was the mechanism by which the ancient ancestor of PHYA, PHYB, and PHYC became triplicated, enabling the evolution of these three genes with different (albeit related) functions? How much chromatin was involved in this(these) event(s), and what control elements or nearby genes were involved.

2 - Subsequent to the divergence of the three PHY from a common ancestor, what has been the evolutionary fate of the surrounding chromatin? Can DNA sequence conservation help to reveal nearby control elements that have been protected by divergence based on functional contraints?

3- What genes now occur near the three PHY? Is there any evidence that neighboring genes are coordinately regulated in conjunction with PHY(s), or interact directly with PHY(s)? Are these genes duplicated or triplicated in parallel with the PHY?