THE PHYTOCHROME GENE FAMILY IN TOMATO INCLUDES A NOVEL SUBFAMILY

Data presented here define five tomato phytochrome genes (PHY) and ind icate the existence of additional PHY in the tomato genome. Portions o f each gene, encoding amino acids 203 through 315 in a consensus amino acid sequence, were amplified by polymerase chain reaction. Four of t hese genes, PHYA, PHYB1, PHYB2 and PHYE, are members of previously ide ntified PHY subfamilies, while the fifth, PHYF, is identified as a mem ber of a new PHY subfamily. PHYA, PHYB1, PHYB2 and PHYE fragments enco de amino acid sequences that share 88% to 98% sequence identity with t heir Arabidopsis counterparts. The PHYF fragment, however, encodes a p olypeptide that shares only 65% to 74% quence identity with previously identified Arabidopsis phytochromes. A phylogenetic analysis suggests that PHYF arose soon after, or perhaps prior to, the origin of angios perms. This analysis leads to the prediction that PHYF might be widesp read among angiosperms, including both monocotyledons and dicotyledons . Each of the five tomato PHY is expressed as a transcript of sufficie nt size to encode a full-length phytochrome apoprotein. Two PHYF trans cripts, 4.4 and 4.7 kb in length, have been detected in 9-day-old ligh t-grown seedlings, consistent with either multiple transcription start sites or differential processing. Analyses of genomic Southern blots hybridized with radiolabelled RNA probes derived from the five tomato PHY, as well as Arabidopsis PHYC, indicate that the tomato genome cont ains as many as 9 to 13 PHY. The tomato PHY family is apparently not o nly different from, but also larger than, the PHY family presently des cribed for Arabidopsis.