The Phytochrome Gene Family in the Stellaria longipes Complex

Abstract

Stellaria longipes is a polymorphic polyploid species distributed in a variety of habitats in North America and parts of Eurasia. It shows considerable amounts and patterns of phenotypic plasticity. We are interested in elucidating the possible role of phytochromes in phenotypic plasticity. Therefore, we characterized the phytochrome gene family in S. longipes and three related species. Using PCR, RT‐PCR, and RACE cloning, we recovered four fragments of PHYA (designated PHYA1, PHYA2, PHYA3, and PHYA4), one PHYB, and one PHYC. PHYA1 shares 99% nucleotide and 98% amino acid identities with PHYA2, except that PHYA2 contains a 561‐bp deletion. PHYA3 shares 94% nucleotide and amino acid identities with PHYA4, except that PHYA3 contains a 3‐bp insertion. However, a portion of PHYA3 and PHYA4 fragments from position at 2140 to the 3′ end of cDNA shares only 77% nucleotide identity, and the remaining portions of both fragments share 98% nucleotide identity with each other. PHYA1 is closely related to PHYA2, and PHYA3 is closely related to PHYA4. PHYA1–A4 fragments are closely related to Arabidopsis PHYA. They have a nucleotide identity of 68%–75% and a deduced amino acid identity of 71%–73% with Arabidopsis PHYA. PHYB fragment shares 68%–70% nucleotide and 73%–74% amino acid identities with Arabidopsis PHYB/D. PHYC fragment shares 62% nucleotide and 56% amino acid identities with Arabidopsis PHYC. On the basis of Southern blots, three members of PHYA, one of PHYB, and one of PHYC were detected in Stellaria by our probes. In Southern blots with probes from the Arabidopsis PHYD, tomato PHYE, and PHYF, no major bands were detected in any genotypes and restriction enzyme digests. These results indicate that the Stellaria PHY family consists of six gene members, which are classified into PHYA, PHYB/D, and PHYC/F subfamilies, but lacks a member of the PHYE subfamily.