Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.

Coffee, tea, and chocolate converge: Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeudet al.sequenced theCoffea canephora(coffee) genome and identified a conserved gene order (see the Perspective by Zamir). Although this species underwent fewer genome duplications than related species, the relevant caffeine genes experienced tandem duplications that expanded their numbers within this species. Scientists have seen similar but independent expansions in distantly related species of tea and cacao, suggesting that caffeine might have played an adaptive role in coffee evolution.Science, this issue p.1181; see also p.1124

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns—one at the base of ‘core leptosporangiates’ and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N₂-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla–cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

The genome of the carnivorous bladderwort plant Utricularia gibba is described here; despite having undergone at least three rounds of whole-genome duplication, its genome is unusually small and virtually devoid of intergenic DNA. Bladderworts are carnivorous plants found in fresh water and damp soil, where they feed on minute prey such as protozoa and rotifers. They lack clearly distinguishable roots, leaves or stems but produce tiny orchid-like flowers. The genome of one of these plants, Utricularia gibba, has now been sequence and analysed. The genome is unusually small (at 82 megabases), in part due to the near absence of intergenic DNA, but it encodes a typical number of genes for a plant and is sufficient to regulate the development and reproduction of a complex organism. Though Although remaining small, the genome has undergone at least three rounds of whole-genome duplication since common ancestry with tomato (Solanum) and grape (Vitis). It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.

Plants sense the presence of potentially competing nearby individuals as a reduction in the red to far‐red ratio of the incoming light. In anticipation of eventual shading, a set of plant responses known as the shade avoidance syndrome (SAS) is initiated soon after detection of this signal by the phytochrome photoreceptors. Here we analyze the function of P HYTOCHROME R A PIDLY R EGULATED 1 ( PAR1) and PAR2 , two Arabidopsis thaliana genes rapidly upregulated after simulated shade perception. These genes encode two closely related atypical basic helix–loop–helix proteins with no previously assigned function in plant development. Using reverse genetic approaches, we show that PAR1 and PAR2 act in the nucleus to broadly control plant development, acting as negative regulators of a variety of SAS responses, including seedling elongation and photosynthetic pigment accumulation. Molecularly, PAR1 and PAR2 act as direct transcriptional repressors of two auxin‐responsive genes, S MALL A UXIN U P R EGULATED 15 ( SAUR15 ) and SAUR68 . Additional results support that PAR1 and PAR2 function in integrating shade and hormone transcriptional networks, rapidly connecting phytochrome‐sensed light changes with auxin responsiveness.

Summary: Carotenoids are isoprenoid pigments that function as photoprotectors, precursors of the hormone abscisic acid (ABA), colorants and nutraceuticals. A major problem for the metabolic engineering of high carotenoid levels in plants is the limited supply of their isoprenoid precursor geranylgeranyl diphosphate (GGPP), formed by condensation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) units usually synthesized by the methylerythritol phosphate (MEP) pathway in plastids. Our earlier work with three of the seven MEP pathway enzymes suggested that the first reaction of the pathway catalyzed by deoxyxylulose 5‐phosphate synthase (DXS) is limiting for carotenoid biosynthesis during tomato (Lycopersicon esculentum) fruit ripening. Here we investigate the contribution of the enzyme hydroxymethylbutenyl diphoshate reductase (HDR), which simultaneously synthesizes IPP and DMAPP in the last step of the pathway. A strong upregulation of HDR gene expression was observed in correlation with carotenoid production during both tomato fruit ripening and Arabidopsis thaliana seedling deetiolation. Constitutive overexpression of the tomato cDNA encoding HDR in Arabidopsis did not increase carotenoid levels in etioplasts. By contrast, light‐grown transgenic plants showed higher carotenoid levels and an enhanced seed dormancy phenotype suggestive of increased ABA levels. The analysis of double transgenic Arabidopsis plants overproducing both the enzyme taxadiene synthase (which catalyzes the production of the non‐native isoprenoid taxadiene from GGPP) and either HDR or DXS showed a twofold stronger effect of HDR in increasing taxadiene levels. Together, the data support a major role for HDR in controlling the production of MEP‐derived precursors for plastid isoprenoid biosynthesis.