Non‐angiosperm phytochromes and the evolution of vascular plants

Abstract

The phytochromes, a class of plant light‐sensing pigments, are a gene family with a long, complex evolutionary history. Angiosperms each have five or more phytochromes (designated A to E in Arabidopsis) with distinct functions as light receptors and only moderate sequence identities for different types within a species. The long‐term challenge taken up here is to trace the origin and function of the various motifs within the angiosperm phytochromes through gymnosperm phytochromes (types N, O and P) and lower plant phytochromes, sometimes reaching even to bacterial progenitor molecules. Particularly intriguing are the findings of homology of a C‐terminal region of phytochromes with bacterial transmitter modules and of a large N‐terminal region with a protein encoded by a gene from the cyanobacterum Synechocystis. Phylogenetic analysis helps to answer general questions such as the times of divergence of mono‐ and dicotyledons, of groups of gymnosperms or of ferns. Phytochrome sequences suggest (1) that mono‐ and dicotyledons became separated 150‐200 million years earlier than indicated by the fossil record and (2) that Ginkgo and Cycas have been separated unexpectedly late from the lineage giving rise to the Pinidae. (3) The status of Psilotum as a close relative of the primeval vascular plants is not supported. Phytochrome gene sequences additionally reveal that (4) moss and fern phytochromes have erratically acquired C‐termini which, though kinase‐like, are different from the common ones and that (5) introns have been lost, gained or shifted in position from algae to angiosperms. Phytochromes promise to be a rich source of phylogenetic information into the future as more sequences and functional data emerge, not least from studies of lower plants.

MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants

“…Moreover, given the high sequence similarity between Gnetum and conifer sequences relative to the average similarity between plant MADS-domain proteins, it seems unlikely that undetected angiosperm genes exist that would dissect the different Gnetum-conifer clades and, thus, would indicate alternative relationships such as Gnetum-angiosperm clades. Finally, our results are in agreement with most other recent phylogeny reconstructions based on molecular markers (6)(7)(8)(9)(10)(11)(12)(13), including the tree we calculated with the sequences of the FLORICAULA͞LEAFY orthologs, although all the former work did not lead to final conclusions concerning the phylogenetic relationships of the taxa in question. Taken together, we suggest that within this work an important aspect of seed plant phylogeny has been identified correctly.…”

“…However, previous phylogeny reconstructions based on different molecular markers obtained from all three plant genomes had difficulties to support this hypothesis. On the contrary, most of the respective phylogenetic trees showed the tendency to place gnetophytes, or Gnetales, as a sister group to conifers rather than to angiosperms or suggested a monophyletic origin of all gymnosperms (6)(7)(8)(9)(10)(11)(12)(13). However, in most cases the statistical support for the alternative groupings was relatively weak, and because some phylogenetic trees gave ambiguous results or even weakly supported the anthophyte hypothesis (14)(15)(16), the relationship between gnetophytes, angiosperms, and conifers has remained an open question so far.…”

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

“…Whether the PHYA/B split occurred earlier in the history of seed plants could not be determined because this tree and other early PHY trees (e.g., Heyer and Gatz, 1992;Clack et al, 1994;Mathews et al, 1995;Pratt et al, 1995) included no gymnosperm PHY. The first trees to include gymnosperm PHY (PHYN, PHYO, and PHYP) suggested the split between PHYA and PHYB was even deeper, predating the divergence of angiosperms from other seed plants; the PHYP sequence from Pinus attached to the branch including PHYB and PHYB-related sequences, while the PHYO sequence from Picea attached below the node uniting PHYA with PHYC sequences (Mathews and Sharrock, 1997;Schneider-Poetsch et al, 1998;Clapham et al, 1999). These trees also included sequences from ferns, lycophytes, and mosses and thus revealed that the divergence between PHYA and PHYB, and their gymnosperm homologs, occurred after the free-sporing groups had originated and diverged from other plants, since none of the sequences from freesporing species attached to branches within the seed plant clade.…”

elongated mesocotyl1, a Phytochrome-Deficient Mutant of Maize

“…The basis of phytochrome action is a reversible photoconversion between a red light (R)-absorbing form (Pr) and a far-red light (FR)-absorbing form (Pfr; Quail, 2002). In lower plants, the family is represented by a small number of nuclear genes (Schneider-Poetsch et al, 1998). However, gene duplication and evolutionary divergence have resulted in the formation of functionally diverse multigene families in flowering plants.…”