Rice PHYC gene: structure, expression, map position and evolution

Although sequences representing members of the phytochrome (phy) family of photoreceptors have been reported in numerous species across the phylogenet ic spectrum, relatively few phytochrome genes (PHY) have been fully charact erized. Using rice, we have cloned and characterized the first PHYC gene fr om a monocot. Comparison of genomic and cDNA PHYC sequences shows that the rice PHYC gene contains three introns in the protein-coding region typical of most angiosperm PHY genes, in contrast to Arabidopsis PHYC, which lacks the third intron. Mapping of the transcription start site and 5'-untranslat ed region of the rice PHYC transcript indicates that it contains an unusual ly long, intronless, 5'-untranslated leader sequence of 715 bp. PHYC mRNA l evels are relatively low compared to PHYA and PHYB mRNAs in rice seedlings, and are similar in dark- and light-treated seedlings, suggesting relativel y low constitutive expression. Genomic mapping shows that the PHYA, PHYB, a nd PHYC genes are all located on chromosome 3 of rice, in synteny with thes e genes in linkage group C (sometimes referred to as linkage group A) of so rghum. Phylogenetic analysis indicates that rice phyC is closely related to sorghum phyC, but relatively strongly divergent from Arabidopsis phyC, the only full-length dicot phyC sequence available.