Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

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Ancestral polyploidy in seed plants and angiosperms

The docking field has come of age. The time is ripe to present the principles of docking, reviewing the current state of the field. Two reasons are largely responsible for the maturity of the computational docking area. First, the early optimism that the very presence of the "correct" native conformation within the list of predicted docked conformations signals a near solution to the docking problem, has been replaced by the stark realization of the extreme difficulty of the next scoring/ranking step. Second, in the last couple of years more realistic approaches to handling molecular flexibility in docking schemes have emerged. As in folding, these derive from concepts abstracted from statistical mechanics, namely, populations. Docking and folding are interrelated. From the purely physical standpoint, binding and folding are analogous processes, with similar underlying principles. Computationally, the tools developed for docking will be tremendously useful for folding. For large, multidomain proteins, domain docking is probably the only rational way, mimicking the hierarchical nature of protein folding. The complexity of the problem is huge. Here we divide the computational docking problem into its two separate components. As in folding, solving the docking problem involves efficient search (and matching) algorithms, which cover the relevant conformational space, and selective scoring functions, which are both efficient and effectively discriminate between native and non-native solutions. It is universally recognized that docking of drugs is immensely important. However, protein-protein docking is equally so, relating to recognition, cellular pathways, and macromolecular assemblies. Proteins function when they are bound to other molecules. Consequently, we present the review from both the computational and the biological points of view. Although large, it covers only partially the extensive body of literature, relating to small (drug) and to large protein-protein molecule docking, to rigid and to flexible. Unfortunately, when reviewing these, a major difficulty in assessing the results is the non-uniformity in the formats in which they are presented in the literature. Consequently, we further propose a way to rectify it here.

Principles of docking: An overview of search algorithms and a guide to scoring functions

Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day–induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

https://science.sciencemag.org/content/sci/early/2006/05/04/science.1126038.full.pdf

CO/FT Regulatory Module Controls Timing of Flowering and Seasonal Growth Cessation in Trees

Genetic Control of Light-inhibited Hypocotyl Elongation in Arabidopsis thaliana (L.) Heynh

Plants are sessile and photo-autotrophic; their entire life cycle is thus strongly influenced by the ever-changing light environment. In order to sense and respond to those fluctuating conditions higher plants possess several families of photoreceptors that can monitor light from UV-B to the near infrared (far-red). The molecular nature of UV-B sensors remains unknown, red (R) and far-red (FR) light is sensed by the phytochromes (phyA-phyE in Arabidopsis) while three classes of UV-A/blue photoreceptors have been identified: cryptochromes, phototropins, and members of the Zeitlupe family (cry1, cry2, phot1, phot2, ZTL, FKF1, and LKP2 in Arabidopsis). Functional specialization within photoreceptor families gave rise to members optimized for a wide range of light intensities. Genetic and photobiological studies performed in Arabidopsis have shown that these light sensors mediate numerous adaptive responses (e.g., phototropism and shade avoidance) and developmental transitions (e.g., germination and flowering). Some physiological responses are specifically triggered by a single photoreceptor but in many cases multiple light sensors ensure a coordinated response. Recent studies also provide examples of crosstalk between the responses of Arabidopsis to different external factors, in particular among light, temperature, and pathogens. Although the different photoreceptors are unrelated in structure, in many cases they trigger similar signaling mechanisms including light-regulated protein-protein interactions or light-regulated stability of several transcription factors. The breath and complexity of this topic forced us to concentrate on specific aspects of photomorphogenesis and we point the readers to recent reviews for some aspects of light-mediated signaling (e.g., transition to flowering).

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Light-regulated plant growth and development.

The effects of different growth regimes on gluconasturtiin concentration in watercress (Nasturtium officinale R Br) were investigated Watercress plantlets at the 5th mature leaf stage (ca 2 weeks old) were exposed to different day and night temperatures, to long (16 h) or short (8 h) days, to red (R) or far-red (FR) light given during the main long day photoperiod, and finally to R or FR light given at the end of the main photoperiod Watercress plants grown under long days contained a 30-40% higher gluconasturtiin concentration and had a higher fresh weight than watercress plants grown under short days Watercress plants grown under long days and temperatures of 15 or 10 degrees C had at least a 50% higher gluconasturtiin concentration, but a lower fresh weight, than that of plants grown at 20 or 25 degrees C Watercress plants grown under metal halide light enriched with R light had approximately a 25-40% higher concentration of gluconasturtiin as compared to the FR-enriched plants Likewise, a brief R light exposure at the end of the main photoperiod resulted in approximately a 25% or higher concentration of gluconasturtiin as compared to a FR end-of-day exposure These data indicate that the concentration of gluconasturtiin in watercress can be significantly increased by growing plants at lower temperatures, under long days, and by exposure to R light

The effect of temperature, photoperiod, and light quality on gluconasturtiin concentration in watercress (Nasturtium officinale R. Br.).

In trees and other woody perennial plants, short days (SDs) typically induce growth cessation, the initiation of cold acclimation, the formation of a terminal bud and bud dormancy. Phytochrome control of SD-induced bud set was investigated in two northern clones of black cottonwood (Populus trichocarpa Torr. & Gray) by using night breaks with red light (R) and far-red light (FR). For both clones (BC-1 and BC-2), SD-induced bud set was prevented when R night breaks as short as 2 min were given in the middle of the night. When night breaks with 2 min of R were immediately followed by 2 min of FR, substantial reversibility of bud set was observed for BC-1 but not for BC-2. By comparing the effects of the R night breaks on bud set and the length of specific internodes, we determined that the R night breaks influenced internode elongation in two opposing ways. First, the addition of a R night break to the SD treatment prevented the cessation of internode elongation that is associated with bud set. Those internodes that would not have elongated under SDs (and would have been found within the terminal bud) elongated in the R treatment. Second, the R night breaks decreased internode length relative to the long-day (LD) control. In contrast to the clonal differences in reversibility that we observed for bud set, the decrease in internode length (i.e. the second effect of R) was R/FR reversible in both clones. Based on these results, we conclude that internode elongation is influenced by two distinct types of phytochrome-mediated response. The first response is a typical response to photpperiod, whereas the second response is a typical “end-of-day” response to light quality. Our results demonstrate that SD-induced bud set in black cottonwood is controlled by phytochrome but that clonal differences have an important influence on the R/FR reversibility of this response. The availability of an experimental system in which SD-induced bud set is R/FR reversible will be valuable for studying the physiological genetics of photoperiodism in trees.

Phytochrome control of short-day-induced bud set in black cottonwood

The phytochrome photoreceptors play important roles in the photoperiodic control of vegetative bud set, growth cessation, dormancy induction, and cold-hardiness in trees. Interestingly, ecotypic differences in photoperiodic responses are observed in many temperate-zone tree species. Northern and southern ecotypes of black cottonwood (Populus trichocarpa Torr. & Gray), for example, exhibit marked differences in the timing of short-day-induced bud set and growth cessation, and these responses are controlled by phytochrome. Therefore, as a first step toward determining the molecular genetic basis of photoperiodic ecotypes in trees, we characterized the phytochrome gene (PHY) family in black cottonwood. We recovered fragments of one PHYA and two PHYB using PCR-based cloning and by screening a genomic library. Results from Southern analyses confirmed that black cottonwood has one PHYA locus and two PHYB loci, which we arbitrarily designated PHYB1 and PHYB2. Phylogenetic analyses which included PHY from black cottonwood, Arabidopsis thaliana and tomato (Solanum lycopersicum) suggest that the PHYB/D duplications in these species occurred independently. When Southern blots were probed with PHYC, PHYE, and PHYE heterologous probes, the strongest bands that we detected were those of black cottonwood PHYA and/or PHYB. These results suggest that black cottonwood lacks members of the PHYC/F and PHYE subfamilies. Although black cottonwood could contain additional PHY that are distantly related to known angiosperm PHY, our results imply that the PHY family of black cottonwood is less complex than that of other well-characterized dicot species such as Arabidopsis and tomato. Based on Southern analyses of five black cottonwood genotypes representing three photoperiodic ecotypes, substantial polymorphism was detected for at least one of the PHYB loci but not for the PHYA locus. The novel character of the PHY family in black cottonwood, as well as the differences in polymorphism we observed between the PHYA and PHYB subfamilies, indicates that a number of fundamental macro- and microevolutionary questions remain to be answered about the PHY family in dicots.

/pdf/evidence-that-the-phytochrome-gene-family-in-black-5869wn8pp3.pdf

Evidence that the phytochrome gene family in black cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies.

Glucosinolates are a class of nitrogen (N) and sulfur (S) containing compounds shown to have cancer-preventing properties in animal models and widely found in crucifer- ous plants. The overall objective of this study was to determine whether N and S fertility affects glucosinolate concentrations in cabbage (Brassica oleracea L. Capitata group). Field studies on a sandy soil low in available N and S were conducted over a 2-year period with both green ('Grand Slam') and red ('Vorox') cabbage cultivars. Treatments evaluated each year were the interactive effects of N (125 and 250 kg·ha -1 ) and S (0, and 110 kg·ha -1 ) fertil- izer application. Yield of both cabbage cultivars increased with increasing N and S in the second year of the study, but not in the fi rst. Tissue N concentrations in heads at harvest increased with N application and tissue S concentrations increased with S application. When S was not applied, tissue S decreased signifi cantly as N rate increased, while N rate had no effect on tissue S concentrations when S was applied. The dominant glucosinolate detected in both cabbage cultivars was glucobrassicin, with indole forms accounting for about 80% of the total glucosinolates regardless of treatment. Tissue N was negatively correlated and tissue S and S to N ratio were positively correlated with total glucosinolate concentration, although all correlations were generally weak (r 2 < 0.5). Total glucosinolates and glucobras- sicin concentrations were maximized in both cultivars at the low N and high S application rates. Except for sinigrin in one of the 2 years, all glucosinolates detected were higher in Vorox than in 'Grand Slam'. Based on these results, glucosinolates in cabbage can be ma- nipulated by cultural management practices as well as genetics. Glucosinolates are secondary nitrogen (N) and sulfur (S) containing compounds in plants that have been studied extensively in recent years for their effects on animal health. While glucosinolates are known to be present in 16 families of plants, most of the edible glucosinolate-containing species are found in the family of Cruciferae (Fahey et al., 2001). About 120 glucosinolate compounds have been identifi ed in plants, although there is only lim- ited information on the specifi c effects of each compound and their breakdown products. Activity of glucosinolates has been linked to increased insect resistance (Fenwick et al., 1983; Wolfson, 1982) as well as stimulation of insect feeding (Fenwick et al., 1983). The compounds and breakdown products have also been shown to be allelopathic and increase disease resistance of plants (Angus et al., 1994; Bending and Lincoln, 1999; Rosa et al., 1997). When ingested, some glucosinolates have been shown to impart a bitter fl avor, cause goitro- genic effects, and reduce meal quality of animal feed (Drewnowski and Gomez-Carneros, 2000; Fenwick et al., 1983). One major positive attribute of glucosino- lates is that they have been shown to inhibit the activity of some chemical carcinogens. The plant enzyme myrosinase is released upon consumption of glucosinolate containing veg- etables and catalyzes glucosinolate hydrolysis (Fenwick et al., 1983). Products of hydrolysis depend on the structure of the glucosinolate. Alkyl and arylalkyl glucosinolates yield mainly isothiocyanates upon myrosinase-catalyzed hydrolysis, whereas indolyl glucosinolates (glucobrassicins) yield primarily indole-3-car- binol or related substituted indole-3-carbinols (Fahey et al., 2001; Fenwick et al., 1989; Mc- Danell et al., 1988). Isothiocyanates as well as indole-3-carbinol are chemopreventive agents against carcinogenesis of the lung and other tissues in laboratory animals, and they exert protective effects such as inhibition of car- cinogen activating enzymes, enhancement of carcinogen detoxifying enzymes, and induction of apoptosis (Hecht, 1999). However, indole- 3-carbinol has also been shown to have tumor promoting activity in animal feeding studies (Fahey and Stephenson, 1999; Hecht, 1999),

/pdf/cabbage-yield-and-glucosinolate-concentrations-as-affected-55wghzm0v5.pdf

Cabbage Yield and Glucosinolate Concentrations as Affected by Nitrogen and Sulfur Fertility

https://works.bepress.com/karin_kettenring/137/download/

Gary Gardner

Papers

The effect of temperature, photoperiod, and light quality on gluconasturtiin concentration in watercress (Nasturtium officinale R. Br.).

Phytochrome control of short-day-induced bud set in black cottonwood

Evidence that the phytochrome gene family in black cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies.

Cabbage Yield and Glucosinolate Concentrations as Affected by Nitrogen and Sulfur Fertility

Effect of light on seed germination of eight wetland Carex species