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Abstract
Phytochromes are encoded by a light-responsive gene family inherent to all plants and the cyanobacterial progenitor of their plasmids. The genome of the plant Oryza sativa (rice) contains a three-membered phytochrome gene family. The region of the genome containing each phytochrome genes was sequenced and subsequently annotated using a method developed here to identify the genes upstream and downstream of each phytochrome gene. A comparative analysis of the phytochrome-containing sequences revealed that, due to the age of the gene duplication events that gave rise to the multi-membered phytochrome gene family, no mechanisms of gene family expansion can be currently detected in the genome. Analysis of the putative promoters of the phytochrome genes revealed that light-regulatory elements were among the most abundantly identified type of regulatory motif within sequences conserved between phytochrome rice/sorghum orthologs.