Carotenoid Crystal Formation in Arabidopsis and Carrot Roots Caused by Increased Phytoene Synthase Protein Levels

Background

As the first pathway-specific enzyme in carotenoid biosynthesis, phytoene synthase (PSY) is a prime regulatory target. This includes a number of biotechnological approaches that have successfully increased the carotenoid content in agronomically relevant non-green plant tissues through tissue-specific PSY overexpression. We investigated the differential effects of constitutive AtPSY overexpression in green and non-green cells of transgenic Arabidopsis lines. This revealed striking similarities to the situation found in orange carrot roots with respect to carotenoid amounts and sequestration mechanism.

Methology/Principal Findings

In Arabidopsis seedlings, carotenoid content remained unaffected by increased AtPSY levels although the protein was almost quantitatively imported into plastids, as shown by western blot analyses. In contrast, non-photosynthetic calli and roots overexpressing AtPSY accumulated carotenoids 10 and 100-fold above the corresponding wild-type tissues and contained 1800 and 500 µg carotenoids per g dry weight, respectively. This increase coincided with a change of the pattern of accumulated carotenoids, as xanthophylls decreased relative to β-carotene and carotene intermediates accumulated. As shown by polarization microscopy, carotenoids were found deposited in crystals, similar to crystalline-type chromoplasts of non-green tissues present in several other taxa. In fact, orange-colored carrots showed a similar situation with increased PSY protein as well as carotenoid levels and accumulation patterns whereas wild white-rooted carrots were similar to Arabidopsis wild type roots in this respect. Initiation of carotenoid crystal formation by increased PSY protein amounts was further confirmed by overexpressing crtB, a bacterial PSY gene, in white carrots, resulting in increased carotenoid amounts deposited in crystals.

Conclusions

The sequestration of carotenoids into crystals can be driven by the functional overexpression of one biosynthetic enzyme in non-green plastids not requiring a chromoplast developmental program as this does not exist in Arabidopsis. Thus, PSY expression plays a major, rate-limiting role in the transition from white to orange-colored carrots.     

A Comprehensive Analysis of Chromoplast Differentiation Reveals Complex Protein Changes Associated with Plastoglobule Biogenesis and Remodeling of Protein Systems in Sweet Orange Flesh

Globular and crystalloid chromoplasts were observed to be region specifically formed in sweet orange (Citrus sinensis) flesh and converted from amyloplasts during fruit maturation, which was associated with the composition of specific carotenoids and the expression of carotenogenic genes. Subsequent isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analyses of purified plastids from the flesh during chromoplast differentiation and senescence identified 1,386 putative plastid-localized proteins, 1,016 of which were quantified by spectral counting. The iTRAQ values reflecting the expression abundance of three identified proteins were validated by immunoblotting. Based on iTRAQ data, chromoplastogenesis appeared to be associated with three major protein expression patterns: (1) marked decrease in abundance of the proteins participating in the translation machinery through ribosome assembly; (2) increase in abundance of the proteins involved in terpenoid biosynthesis (including carotenoids), stress responses (redox, ascorbate, and glutathione), and development; and (3) maintenance of the proteins for signaling and DNA and RNA. Interestingly, a strong increase in abundance of several plastoglobule-localized proteins coincided with the formation of plastoglobules in the chromoplast. The proteomic data also showed that stable functioning of protein import, suppression of ribosome assembly, and accumulation of chromoplast proteases are correlated with the amyloplast-to-chromoplast transition; thus, these processes may play a collective role in chromoplast biogenesis and differentiation. By contrast, the chromoplast senescence process was inferred to be associated with significant increases in stress response and energy supply. In conclusion, this comprehensive proteomic study identified many potentially new plastid-localized proteins and provides insights into the potential developmental and molecular mechanisms underlying chromoplast biogenesis, differentiation, and senescence in sweet orange flesh.Chromoplasts are special organelles with superior ability to synthesize and store massive amounts of carotenoids, bringing vivid red, orange, and yellow colors to many flowers, fruits, and vegetables (Li and Yuan, 2013). Chromoplasts exhibit various morphologies, such as crystalline, globular, tubular, and membranous structures (Egea et al., 2010). The relationship between the architecture and carotenoid composition has been well stated in diverse pepper (Capsicum annuum) and tomato (Solanum lycopersicum) fruits (Kilcrease et al., 2013; Nogueira et al., 2013). Crystalline bodies have been observed in carrot (Daucus carota; Frey-Wyssling and Schwegler, 1965) and tomato (Harris and Spurr, 1969), which predominantly consist of β-carotene and lycopene, respectively. Globular and/or tubular-globular chromoplasts, in which numerous lipid droplets (also named plastoglobules), which act as passive storage compartments for triglycerides, sterol ester, and some pigments, are accumulated, were described for yellow fruits from kiwi (Actinidia deliciosa), papaya (Carica papaya), and mango (Mangifera indica), which contain lutein, β-cryptoxanthin, and β-carotene as the major pigments, respectively (Vasquez-Caicedo et al., 2006; Montefiori et al., 2009; Schweiggert et al., 2011). Carotenoid composition has been reported to be regulated by the expression of carotenogenic genes in the flesh of various citrus fruits differing in their internal colors (Fanciullino et al., 2006, 2008). Chromoplasts are frequently derived from fully developed chloroplasts, as seen during fruit ripening from green to red or yellow fruits in tomato and pepper (Egea et al., 2010). In some cases, chromoplasts also arise from nonphotosynthetic plastids, such as colorless proplastids, leucoplasts, or amyloplasts (Knoth et al., 1986; Schweiggert et al., 2011). To date, most studies on chromoplast differentiation have been focused on the synthesis of carotenoids by combining biochemical and molecular analyses (Cazzonelli and Pogson, 2010; Egea et al., 2010; Bian et al., 2011; Li and Yuan, 2013), and little is known about the molecular mechanisms underlying chromoplast biogenesis (Li and Yuan, 2013).Recently, proteomics has become an efficient tool to study the protein composition of subcellular organelles such as chromoplasts and their dynamic changes during the development of a particular plant organ/tissue. The majority of chromoplast-related studies are concerned with the functions of these organelles in various crops, such as pepper, tomato, watermelon (Citrulis lanatus), carrot, cauliflower (Brassica oleracea), and papaya (Siddique et al., 2006; Wang et al., 2013). However, only a few of such studies addressed the mechanisms underlying plastid differentiation, such as the transition from proplastid to chloroplast in maize (Zea mays; Majeran et al., 2010), from etioplast to chloroplast in pea (Pisum sativum; Kanervo et al., 2008) and rice (Oryza sativa; Kleffmann et al., 2007), and from chloroplast to chromoplast in tomato (Barsan et al., 2012). In tomato, chromoplastogenesis appears to be associated with major metabolic shifts, including a strong decrease in abundance of the proteins involved in light reaction and an increase in terpenoid biosynthesis and stress-response proteins (Barsan et al., 2012). These changes in proteins are in agreement with the structural changes occurring in tomato during fruit ripening, which is characterized by the loss of chlorophyll and the synthesis of colored compounds. Chromoplast differentiation from nonphotosynthetic plastids occurs frequently in a number of plant tissues, such as watermelon flesh and carrot root (Kim et al., 2010; Wang et al., 2013). However, to the best of our knowledge, no large-scale proteomic study for understanding this developmental process has been reported.Citrus is one of the most economically important fruit crops in the world. Different from the model fruit tomato, which represents climacteric fruits, citrus shows nonclimacteric characteristics during fruit maturation. Additionally, citrus fruits exhibit a unique anatomical fruit structure consisting of two major sections, the pericarp and the edible flesh. Considerable progress has been made in the understanding of chromoplast differentiation in the pericarp of citrus fruits (Eilati et al., 1969; Iglesias et al., 2007), which is a process similar to that of tomato and pepper (Egea et al., 2010). However, little is known about the molecular basis of chromoplast differentiation in the edible flesh, even though there is increasing evidence suggesting an essential role of carotenoid synthesis in inducing chromoplast differentiation (Egea et al., 2010; Bian et al., 2011; Li and Yuan, 2013). Recently, we successfully isolated and purified intact chromoplasts containing a large number of plastoglobules from the flesh of sweet orange (Citrus sinensis) fruits at the maturation stage (Zeng et al., 2011). The same method has also been used successfully to isolate plastids from sweet orange flesh in earlier maturation stages (Zeng et al., 2014), thus making comparative and quantitative proteomic analyses of plastid differentiation possible. In this study, we investigated how ultrastructural changes of plastids/chromoplasts during sweet orange fruit maturation might be associated with changes in the composition of carotenoids and the expression of carotenogenic genes in red and yellow flesh of the fruits. Furthermore, we employed the isobaric tag for relative and absolute quantitation (iTRAQ)-based technology to investigate how protein compositional changes might be correlated with metabolic and structural changes in the plastids of sweet orange flesh during their transformation from amyloplasts to chromoplasts.     

Red Bell Pepper Chromoplasts Exhibit in Vitro Import Competency and Membrane Targeting of Passenger Proteins from the Thylakoidal Sec and ΔpH Pathways but Not the Chloroplast Signal Recognition Particle Pathway

Chloroplast to chromoplast development involves new synthesis and plastid localization of nuclear-encoded proteins, as well as changes in the organization of internal plastid membrane compartments. We have demonstrated that isolated red bell pepper (Capsicum annuum) chromoplasts contain the 75-kD component of the chloroplast outer envelope translocon (Toc75) and are capable of importing chloroplast precursors in an ATP-dependent fashion, indicating a functional general import apparatus. The isolated chromoplasts were able to further localize the 33- and 17-kD subunits of the photosystem II O₂-evolution complex (OE33 and OE17, respectively), lumen-targeted precursors that utilize the thylakoidal Sec and ΔpH pathways, respectively, to the lumen of an internal membrane compartment. Chromoplasts contained the thylakoid Sec component protein, cpSecA, at levels comparable to chloroplasts. Routing of OE17 to the lumen was abolished by ionophores, suggesting that routing is dependent on a transmembrane ΔpH. The chloroplast signal recognition particle pathway precursor major photosystem II light-harvesting chlorophyll a/b protein failed to associate with chromoplast membranes and instead accumulated in the stroma following import. The Pftf (plastid fusion/translocation factor), a chromoplast protein, integrated into the internal membranes of chromoplasts during in vitro assays, and immunoblot analysis indicated that endogenous plastid fusion/translocation factor was also an integral membrane protein of chromoplasts. These data demonstrate that the internal membranes of chromoplasts are functional with respect to protein translocation on the thylakoid Sec and ΔpH pathways.Plastids are developmentally related organelles capable of interconversion among a variety of structurally and biochemically distinct forms in response to both environmental and tissue-specific cues (Whatley, 1978; Thomson and Whatley, 1980). Formation of chromoplasts in many fruits is one striking example of this plasticity. Heavily pigmented, photosynthetically inactive chromoplasts frequently develop from chloroplasts during ripening. This conversion involves dramatic changes in the organization and composition of the internal plastid compartment, which include the loss of proteins involved in carbon fixation in the stroma and replacement with chromoplast-specific proteins, the breakdown of the photosynthetic thylakoid membranes and loss of proteins involved in light capture and electron transfer, and, in some cases, the formation of new membranes (Spurr and Harris, 1968; Camara and Brangeon, 1981; Piechulla et al., 1987; Kuntz et al., 1989).Chromoplast formation is an active rather than simply a degradative process. New proteins, specific to or enhanced in chromoplasts, are synthesized and compartmentalized in the plastid (Camara et al., 1995; Price et al., 1995). Most chromoplast proteins are predicted to be nuclear encoded, translated on cytoplasmic ribosomes, and posttranslationally imported into the plastid, as are nuclear-encoded chloroplast proteins. Import of chloroplast proteins occurs via a general import machinery that appears to mediate translocation of most or all proteins that are delivered to the chloroplast stroma, either as a final destination or as an intermediate location (Cline and Henry, 1996; Robinson and Mant, 1997; Schnell, 1998). Proteins are targeted to the general import pathway by an N-terminal extension that is cleaved upon import, resulting in the appearance of a processed protein of reduced M_r. Presumably, the import of proteins into chromoplasts is accomplished by the same machinery that is responsible for import of proteins into chloroplasts, although this has never been directly examined.In some chromoplasts an extensive set of internal membranes accumulates, replacing the thylakoids. For example, in the fibrillar-type chromoplast of bell pepper (Capsicum annuum), the photosynthetic membranes are replaced by membranous sheets and vesicles in addition to the carotenoid-rich plastoglobules and fibrils (Spurr and Harris, 1968; Laborde and Spurr, 1973; Camara and Brangeon, 1981; Deruere et al., 1994). The often extensive internal membranes are the site of synthesis of keto-xanthophylls, which constitute the major carotenoids of red fruit (Bouvier et al., 1994).Our interests are in the biogenesis of the internal membranes of plastids, in particular the proteins that are integral to the bilayer, as well as those located in the luminal compartment formed by the bilayer. In chloroplasts, proteins destined for the thylakoid membrane or lumen are routed from the stroma into the thylakoid membrane and lumen by one of at least four distinct mechanisms: the ΔpH, chloroplast SRP, thylakoid Sec pathways, and an apparently spontaneous insertion mechanism (for review, see Cline and Henry, 1996; Robinson and Mant, 1997; Schnell, 1998). In view of the extensive internal membrane system of bell pepper chromoplasts, one would expect the presence of proteins and accompanying translocation machinery in these membranes. However, no chromoplast-specific proteins have been conclusively demonstrated to be either integral or luminal to these membranes.One protein, Pftf (plastid fusion/translocation factor), predicted to be membrane anchored by sequence analysis, has been purified from the stromal compartment of pepper chromoplasts (Hugueney et al., 1995). This raised the possibility that mature chromoplasts lack the ability to localize proteins into/across internal membranes. To address this question we developed a method for isolating protein import-competent chromoplasts from bell peppers. Immunoblotting confirmed that these chromoplasts contain known translocation machinery components. Chromoplasts were assayed in vitro for their ability to import and localize passenger proteins from the three known protein-machinery-dependent thylakoid-targeting pathways. We found mature chromoplasts to be capable of membrane targeting of proteins that utilize the thylakoidal Sec and ΔpH pathways but not capable of inserting a membrane protein, LHCP, which utilizes the chloroplast SRP pathway. Pftf was inserted into the membranes of these chromoplasts in a manner similar to that observed in chloroplasts, and resident Pftf was also found to be integrally associated with chromoplast membranes. The precise role of these pathways in the formation of bell pepper chromoplasts remains to be fully elucidated.     

Restriction enzyme analysis of tomato chloroplast and chromoplast DNA

Plastid DNA was isolated from the chloroplasts of tomato (Lycopersicon esculentum var Traveler 76) leaves and the chromoplasts of ripe tomato fruit. Comparisons of the two DNAs were made by restriction endonuclease analysis using PvuII, HpaI, and Bg1I. No differences in the electrophoretic banding patterns of the restricted plastid DNAs were detected, indicating that no major rearrangements, losses, or gains of plastid DNA accompany the transition from chloroplast to chromoplast.     

An ATP synthase harboring an atypical γ–subunit is involved in ATP synthesis in tomato fruit chromoplasts

Chromoplasts are non‐photosynthetic plastids specialized in the synthesis and accumulation of carotenoids. During fruit ripening, chloroplasts differentiate into photosynthetically inactive chromoplasts in a process characterized by the degradation of the thylakoid membranes, and by the active synthesis and accumulation of carotenoids. This transition renders chromoplasts unable to photochemically synthesize ATP, and therefore these organelles need to obtain the ATP required for anabolic processes through alternative sources. It is widely accepted that the ATP used for biosynthetic processes in non‐photosynthetic plastids is imported from the cytosol or is obtained through glycolysis. In this work, however, we show that isolated tomato (Solanum lycopersicum) fruit chromoplasts are able to synthesize ATP de novo through a respiratory pathway using NADPH as an electron donor. We also report the involvement of a plastidial ATP synthase harboring an atypical γ–subunit induced during ripening, which lacks the regulatory dithiol domain present in plant and algae chloroplast γ–subunits. Silencing of this atypical γ–subunit during fruit ripening impairs the capacity of isolated chromoplast to synthesize ATP de novo. We propose that the replacement of the γ–subunit present in tomato leaf and green fruit chloroplasts by the atypical γ–subunit lacking the dithiol domain during fruit ripening reflects evolutionary changes, which allow the operation of chromoplast ATP synthase under the particular physiological conditions found in this organelle.     

Phylogeographic patterns, genetic affinities and morphological differentiation between Epipactis helleborine and related lineages in a Mediterranean glacial refugium

Background and Aims

In the Mediterranean basin, the Italian peninsula has been suggested to be one of the most important glacial refugia for temperate tree species. The orchid genus Epipactis is widely represented in the Italian peninsula by widespread species and several endemic, localized taxa, including selfing and outcrossing taxa. Here the phylogenetic and phylogeographic relationships in a group of closely related taxa in Epipactis are investigated with the aim of understanding the role of this refugial area for cladogenesis and speciation in herbaceous species, such as terrestrial orchids.

Methods

Ribosomal DNA (rDNA) was employed to assess phylogenetic relationships, and plastid sequence variation in the rbcL–accD spacer was used to reveal phylogeographic patterns among plastid haplotypes using a parsimony network.

Key Results

Low genetic variation and shared ribotypes were detected in rDNA, whereas high levels of sequence variation and a strong phylogeographic structure were found in the examined plastid region. The parsimony plastid haplotype network identified two main haplotype groups, one including E. atrorubens/microphylla/muelleri/leptochila and the other including all accessions of E. helleborine and several localized and endemic taxa, with a combination of widespread and rare haplotypes detected across the Italian peninsula. A greater genetic divergence separated the Italian and other European accessions of E. helleborine.

Conclusions

Phylogenetic and phylogeographic patterns support a working hypothesis in which the Italian peninsula has only recently been colonized by Epipactis, probably during the most recent phase of the Quaternary age and, nevertheless, it acted as a remarkable centre of diversification for this orchid lineage. Changes in pollination strategy and recurrent shifts in mating system (from allogamy to autogamy) could have represented the mechanism promoting this rapid diversification and the observed high taxonomic complexity detected in the E. helleborine species complex.     

Tomato Fruit Chromoplasts Behave as Respiratory Bioenergetic Organelles during Ripening

During tomato (Solanum lycopersicum) fruit ripening, chloroplasts differentiate into photosynthetically inactive chromoplasts. It was recently reported that tomato chromoplasts can synthesize ATP through a respiratory process called chromorespiration. Here we show that chromoplast oxygen consumption is stimulated by the electron donors NADH and NADPH and is sensitive to octyl gallate (Ogal), a plastidial terminal oxidase inhibitor. The ATP synthesis rate of isolated chromoplasts was dependent on the supply of NAD(P)H and was fully inhibited by Ogal. It was also inhibited by the proton uncoupler carbonylcyanide m-chlorophenylhydrazone, suggesting the involvement of a chemiosmotic gradient. In addition, ATP synthesis was sensitive to 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, a cytochrome b₆f complex inhibitor. The possible participation of this complex in chromorespiration was supported by the detection of one of its components (cytochrome f) in chromoplasts using immunoblot and immunocytochemical techniques. The observed increased expression of cytochrome c₆ during ripening suggests that it could act as electron acceptor of the cytochrome b₆f complex in chromorespiration. The effects of Ogal on respiration and ATP levels were also studied in tissue samples. Oxygen uptake of mature green fruit and leaf tissues was not affected by Ogal, but was inhibited increasingly in fruit pericarp throughout ripening (up to 26% in red fruit). Similarly, Ogal caused a significant decrease in ATP content of red fruit pericarp. The number of energized mitochondria, as determined by confocal microscopy, strongly decreased in fruit tissue during ripening. Therefore, the contribution of chromoplasts to total fruit respiration appears to increase in late ripening stages.Chromoplasts are plastids specialized in the production and accumulation of carotenoids, conferring color to many fruits and flowers. During tomato (Solanum lycopersicum) fruit ripening, chloroplasts differentiate into chromoplasts in a process that involves the dismantling of the photosynthetic apparatus and a massive synthesis and deposition of lycopene (Camara et al., 1995). Chromoplasts show a barely studied respiratory process, first reported for daffodil (Narcissus pseudonarcissus) chromoplasts and called chromorespiration, which consists of a membrane-bound redox pathway associated with carotenoid desaturation and results in oxygen uptake activity (Nievelstein et al., 1995). The most likely oxidase involved in this respiratory activity is the plastidial terminal oxidase (PTOX), a plastoquinol oxidase homologous to the mitochondrial alternative oxidase (AOX; Carol et al., 1999; Wu et al., 1999). According to its role in chromorespiration and in carotenoid biosynthesis, the expression of PTOX increases during the ripening process of tomato and bell pepper (Capsicum annuum) fruits (Josse et al., 2003), in parallel to chromoplast differentiation. PTOX has been characterized in vitro and it has been reported to be inhibited by pyrogallol analogs, specially by octyl gallate (Ogal; Josse et al., 2000). In vivo, PTOX has been studied mainly in chloroplasts. PTOX not only participates in carotenoid biosynthesis in chloroplasts but is also involved in chlororespiration, an electron transport chain present in thylakoids that shares plastoquinone with the photosynthetic electron transport chain (Carol and Kuntz, 2001; McDonald et al., 2011).In daffodil chromoplast homogenates (Nievelstein et al., 1995) as well as in isolated tomato fruit chromoplasts (Pateraki et al., 2013), NAD(P)H acts as an electron donor for chromorespiration, indicating the participation of NAD(P)H plastoquinone oxidoreductase activity. Considering that tomato fruit chromoplasts derive from chloroplasts, it is possible that some components of the chromoplastic redox pathway could originate from chlororespiration, such as the NAD(P)H:plastoquinone-reductase complex (NDH), which could act as the electron entrance. However, the enzymes involved in chromorespiration are not well known. It was also reported that the oxygen uptake activity of daffodil chromoplast homogenates was sensitive to the classic uncoupler 2,4-dinitrophenol (Nievelstein et al., 1995), and this observation led to the proposal that chromorespiration could be linked to membrane energization. Morstadt et al. (2002) found that liposomes containing daffodil chromoplast proteins and energized by an acid-base transition were able to produce ATP through a chemiosmotic mechanism, demonstrating that daffodil chromoplasts contain a functional H⁺-ATP synthase complex. We recently reported that isolated chromoplasts from tomato fruits can synthesize ATP de novo (Pateraki et al., 2013). This process is dependent on an ATP synthase complex containing an atypical γ-subunit without the regulatory dithiol domain, which may be active using lower proton gradients than those present in the chloroplast (Pateraki et al., 2013). This finding is consistent with proteomic analyses that reveal that several proteins related to electron transport and ATP production are present in chromoplasts of ripe fruits, like ATP synthase, some subunits of the NDH complex, and the cytochrome b₆f complex (Barsan et al., 2012; Wang et al., 2013).Several anabolic pathways that require ATP and reducing agents are active in ripe fruit chromoplasts, such as synthesis of carotenoids, lipids (glycolipids, phospholipids, and sterols), and the shikimate pathway (Bian et al., 2011; Angaman et al., 2012). On the other hand, the ATP synthesis capacity of mitochondria in ripe fruit is low, because its membrane potential diminishes during ripening as a result of the increasing activity of the mitochondrial uncoupling protein (Almeida et al., 1999; Costa et al., 1999). This fact raised the question of whether chromorespiration could play a significant role in the production of ATP at the last stages of ripening. To our knowledge, the ATP synthesis rates of chromoplasts have not been quantified; therefore, it was uncertain whether the endogenous production could provide ATP in significant amounts to address the energy requirements of the chromoplasts. Moreover, there was no information about the quantitative contribution of chromorespiration to total fruit tissue respiration. This work aimed to deepen the study of the chromorespiratory process in isolated tomato fruit chromoplasts and to analyze the relative participation of this pathway in the overall respiration and ATP levels of fruit pericarp in vivo.     

Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

Background and Aims

Two closely related, wild tomato-like nightshade species, Solanum lycopersicoides and Solanum sitiens, inhabit a small area within the Atacama Desert region of Peru and Chile. Each species possesses unique traits, including abiotic and biotic stress tolerances, and can be hybridized with cultivated tomato. Conservation and utilization of these tomato relatives would benefit from an understanding of genetic diversity and relationships within and between populations.

Methods

Levels of genetic diversity and population genetic structure were investigated by genotyping representative accessions of each species with a set of simple sequence repeat (SSR) and allozyme markers.

Key Results

As expected for self-incompatible species, populations of S. lycopersicoides and S. sitiens were relatively diverse, but contained less diversity than the wild tomato Solanum chilense, a related allogamous species native to this region. Populations of S. lycopersicoides were slightly more diverse than populations of S. sitiens according to SSRs, but the opposite trend was found with allozymes. A higher coefficient of inbreeding was noted in S. sitiens. A pattern of isolation by distance was evident in both species, consistent with the highly fragmented nature of the populations in situ. The populations of each taxon showed strong geographical structure, with evidence for three major groups, corresponding to the northern, central and southern elements of their respective distributions.

Conclusions

This information should be useful for optimizing regeneration strategies, for sampling of the populations for genes of interest, and for guiding future in situ conservation efforts.     

GPT2: a glucose 6-phosphate/phosphate translocator with a novel role in the regulation of sugar signalling during seedling development

Background and Aims

GPT2, a glucose 6-phosphate/phosphate translocator, plays an important role in environmental sensing in mature leaves of Arabidopsis thaliana. Its expression has also been detected in arabidopsis seeds and seedlings. In order to examine the role of this protein early in development, germination and seedling growth were studied.

Methods

Germination, greening and establishment of seedlings were monitored in both wild-type Arabidopsis thaliana and in a gpt2 T-DNA insertion knockout line. Seeds were sown on agar plates in the presence or absence of glucose and abscisic acid. Relative expression of GPT2 in seedlings was measured using quantitative PCR.

Key Results

Plants lacking GPT2 expression were delayed (25–40 %) in seedling establishment, specifically in the process of cotyledon greening (rather than germination). This phenotype could not be rescued by glucose in the growth medium, with greening being hypersensitive to glucose. Germination itself was, however, hyposensitive to glucose in the gpt2 mutant.

Conclusions

The expression of GPT2 modulates seedling development and plays a crucial role in determining the response of seedlings to exogenous sugars during their establishment. This allows us to conclude that endogenous sugar signals function in controlling germination and the transition from heterotrophic to autotrophic growth, and that the partitioning of glucose 6-phosphate, or related metabolites, between the cytosol and the plastid modulates these developmental responses.     

Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes

Background and Aims

Here evidence for reticulation in the pantropical orchid genus Polystachya is presented, using gene trees from five nuclear and plastid DNA data sets, first among only diploid samples (homoploid hybridization) and then with the inclusion of cloned tetraploid sequences (allopolyploids). Two groups of tetraploids are compared with respect to their origins and phylogenetic relationships.

Methods

Sequences from plastid regions, three low-copy nuclear genes and ITS nuclear ribosomal DNA were analysed for 56 diploid and 17 tetraploid accessions using maximum parsimony and Bayesian inference. Reticulation was inferred from incongruence between gene trees using supernetwork and consensus network analyses and from cloning and sequencing duplicated loci in tetraploids.

Key Results

Diploid trees from individual loci showed considerable incongruity but little reticulation signal when support from more than one gene tree was required to infer reticulation. This was coupled with generally low support in the individual gene trees. Sequencing the duplicated gene copies in tetraploids showed clearer evidence of hybrid evolution, including multiple origins of one group of tetraploids included in the study.

Conclusions

A combination of cloning duplicate gene copies in allotetraploids and consensus network comparison of gene trees allowed a phylogenetic framework for reticulation in Polystachya to be built. There was little evidence for homoploid hybridization, but our knowledge of the origins and relationships of three groups of allotetraploids are greatly improved by this study. One group showed evidence of multiple long-distance dispersals to achieve a pantropical distribution; another showed no evidence of multiple origins or long-distance dispersal but had greater morphological variation, consistent with hybridization between more distantly related parents.     

Phylogenetic analyses provide the first insights into the evolution of OVATE family proteins in land plants

Background and Aims

The OVATE gene encodes a nuclear-localized regulatory protein belonging to a distinct family of plant-specific proteins known as the OVATE family proteins (OFPs). OVATE was first identified as a key regulator of fruit shape in tomato, with nonsense mutants displaying pear-shaped fruits. However, the role of OFPs in plant development has been poorly characterized.

Methods

Public databases were searched and a total of 265 putative OVATE protein sequences were identified from 13 sequenced plant genomes that represent the major evolutionary lineages of land plants. A phylogenetic analysis was conducted based on the alignment of the conserved OVATE domain from these 13 selected plant genomes. The expression patterns of tomato SlOFP genes were analysed via quantitative real-time PCR. The pattern of OVATE gene duplication resulting in the expansion of the gene family was determined in arabidopsis, rice and tomato.

Key Results

Genes for OFPs were found to be present in all the sampled land plant genomes, including the early-diverged lineages, mosses and lycophytes. Phylogenetic analysis based on the amino acid sequences of the conserved OVATE domain defined 11 sub-groups of OFPs in angiosperms. Different evolutionary mechanisms are proposed for OVATE family evolution, namely conserved evolution and divergent expansion. Characterization of the AtOFP family in arabidopsis, the OsOFP family in rice and the SlOFP family in tomato provided further details regarding the evolutionary framework and revealed a major contribution of tandem and segmental duplications towards expansion of the OVATE gene family.

Conclusions

This first genome-wide survey on OFPs provides new insights into the evolution of the OVATE protein family and establishes a solid base for future functional genomics studies on this important but poorly characterized regulatory protein family in plants.     

New insights into Trimezieae (Iridaceae) phylogeny: what do molecular data tell us?

Background and Aims

The Neotropical tribe Trimezieae are taxonomically difficult. They are generally characterized by the absence of the features used to delimit their sister group Tigridieae. Delimiting the four genera that make up Trimezieae is also problematic. Previous family-level phylogenetic analyses have not examined the monophyly of the tribe or relationships within it. Reconstructing the phylogeny of Trimezieae will allow us to evaluate the status of the tribe and genera and to examine the suitability of characters traditionally used in their taxonomy.

Methods

Maximum parsimony and Bayesian phylogenetic analyses are presented for 37 species representing all four genera of Trimezieae. Analyses were based on nrITS sequences and a combined plastid dataset. Ancestral character state reconstructions were used to investigate the evolution of ten morphological characters previously considered taxonomically useful.

Key Results

Analyses of nrITS and plastid datasets strongly support the monophyly of Trimezieae and recover four principal clades with varying levels of support; these clades do not correspond to the currently recognized genera. Relationships within the four clades are not consistently resolved, although the conflicting resolutions are not strongly supported in individual analyses. Ancestral character state reconstructions suggest considerable homoplasy, especially in the floral characters used to delimit Pseudotrimezia.

Conclusions

The results strongly support recognition of Trimezieae as a tribe but suggest that both generic- and species-level taxonomy need revision. Further molecular analyses, with increased sampling of taxa and markers, are needed to support any revision. Such analyses will help determine the causes of discordance between the plastid and nuclear data and provide a framework for identifying potential morphological synapomorphies for infra-tribal groups. The results also suggest Trimezieae provide a promising model for evolutionary research.     

Influence of plant maturity, shoot reproduction and sex on vegetative growth in the dioecious plant Urtica dioica

Background and Aims

Stinging nettle (Urtica dioica) is a herbaceous, dioecious perennial that is widely distributed around the world, reproduces both sexually and asexually, and is characterized by rapid growth. This work was aimed at evaluating the effects of plant maturity, shoot reproduction and sex on the growth of leaves and shoots.

Methods

Growth rates of apical shoots, together with foliar levels of phytohormones (cytokinins, auxins, absicisic acid, jasmonic acid and salicylic acid) and other indicators of leaf physiology (water contents, photosynthetic pigments, α-tocopherol and F_v/F_m ratios) were measured in juvenile and mature plants, with a distinction made between reproductive and non-reproductive shoots in both males and females. Vegetative growth rates were not only evaluated in field-grown plants, but also in cuttings obtained from these plants. All measurements were performed during an active vegetative growth phase in autumn, a few months after mature plants reproduced during spring and summer.

Key Results

Vegetative growth rates in mature plants were drastically reduced compared with juvenile ones (48 % and 78 % for number of leaves and leaf biomass produced per day, respectively), which was associated with a loss of photosynthetic pigments (up to 24 % and 48 % for chlorophylls and carotenoids, respectively) and increases of α-tocopherol (up to 2·7-fold), while endogenous levels of phytohormones did not differ between mature and juvenile plants. Reductions in vegetative growth were particularly evident in reproductive shoots of mature plants, and occurred similarly in both males and females.

Conclusions

It is concluded that (a) plant maturity reduces vegetative growth in U. dioica, (b) effects of plant maturity are evident both in reproductive and non-reproductive shoots, but particularly in the former, and (c) these changes occur similarly in both male and female plants.     

Evidence for Transitional Stages in the Evolution of Euglenid Group II Introns and Twintrons in the Monomorphina aenigmatica Plastid Genome

Background

Photosynthetic euglenids acquired their plastid by secondary endosymbiosis of a prasinophyte-like green alga. But unlike its prasinophyte counterparts, the plastid genome of the euglenid Euglena gracilis is riddled with introns that interrupt almost every protein-encoding gene. The atypical group II introns and twintrons (introns-within-introns) found in the E. gracilis plastid have been hypothesized to have been acquired late in the evolution of euglenids, implying that massive numbers of introns may be lacking in other taxa. This late emergence was recently corroborated by the plastid genome sequences of the two basal euglenids, Eutreptiella gymnastica and Eutreptia viridis, which were found to contain fewer introns.

Methodology/Principal Findings

To gain further insights into the proliferation of introns in euglenid plastids, we have characterized the complete plastid genome sequence of Monomorphina aenigmatica, a freshwater species occupying an intermediate phylogenetic position between early and late branching euglenids. The M. aenigmatica UTEX 1284 plastid genome (74,746 bp, 70.6% A+T, 87 genes) contains 53 intron insertion sites, of which 41 were found to be shared with other euglenids including 12 of the 15 twintron insertion sites reported in E. gracilis.

Conclusions

The pattern of insertion sites suggests an ongoing but uneven process of intron gain in the lineage, with perhaps a minimum of two bursts of rapid intron proliferation. We also identified several sites that represent intermediates in the process of twintron evolution, where the external intron is in place, but not the internal one, offering a glimpse into how these convoluted molecular contraptions originate.     

A world-wide perspective on crucifer speciation and evolution: phylogenetics,biogeography and trait evolution in tribe Arabideae

Background and Aims

Tribe Arabideae are the most species-rich monophyletic lineage in Brassicaceae. More than 500 species are distributed in the majority of mountain and alpine regions worldwide. This study provides the first comprehensive phylogenetic analysis for the species assemblage and tests for association of trait and characters, providing the first explanations for the enormous species radiation since the mid Miocene.

Methods

Phylogenetic analyses of DNA sequence variation of nuclear encoded loci and plastid DNA are used to unravel a reliable phylogenetic tree. Trait and ancestral area reconstructions were performed and lineage-specific diversification rates were calculated to explain various radiations in the last 15 Myr in space and time.

Key Results

A well-resolved phylogenetic tree demonstrates the paraphyly of the genus Arabis and a new systematic concept is established. Initially, multiple radiations involved a split between lowland annuals and mountain/alpine perennial sister species. Subsequently, increased speciation rates occur in the perennial lineages. The centre of origin of tribe Arabideae is most likely the Irano-Turanian region from which the various clades colonized the temperate mountain and alpine regions of the world.

Conclusions

Mid Miocene early diversification started with increased speciation rates due to the emergence of various annual lineages. Subsequent radiations were mostly driven by diversification within perennial species during the Pliocene, but increased speciation rates also occurred during that epoch. Taxonomic concepts in Arabis are still in need of a major taxonomic revision to define monophyletic groups.     

Natural foliar variegation without costs? The case of Begonia

Background and Aims

Foliar variegation is recognized as arising from two major mechanisms: leaf structure and pigment-related variegation. Begonia has species with a variety of natural foliar variegation patterns, providing diverse examples of this phenomenon. The aims of this work are to elucidate the mechanisms underlying different foliar variegation patterns in Begonia and to determine their physiological consequences.

Methods

Six species and one cultivar of Begonia were investigated. Light and electron microscopy revealed the leaf structure and ultrastructure of chloroplasts in green and light areas of variegated leaves. Maximum quantum yields of photosystem II were measured by chlorophyll fluorescence. Comparison with a cultivar of Ficus revealed key features distinguishing variegation mechanisms.

Key Results

Intercellular space above the chlorenchyma is the mechanism of variegation in these Begonia. This intercellular space can be located (a) below the adaxial epidermis or (b) below the adaxial water storage tissue (the first report for any taxa), creating light areas on a leaf. In addition, chlorenchyma cell shape and chloroplast distribution within chlorenchyma cells differ between light and green areas. Chloroplasts from both areas showed dense stacking of grana and stroma thylakoid membranes. The maximum quantum yield did not differ significantly between these areas, suggesting minimal loss of function with variegation. However, the absence of chloroplasts in light areas of leaves in the Ficus cultivar led to an extremely low quantum yield.

Conclusions

Variegation in these Begonia is structural, where light areas are created by internal reflection between air spaces and cells in a leaf. Two forms of air space structural variegation occur, distinguished by the location of the air spaces. Both forms may have a common origin in development where dermal tissue becomes loosely connected to mesophyll. Photosynthetic functioning is retained in light areas, and these areas do not include primary veins, potentially limiting the costs of variegation.     

Origin of the invasive Arundo donax (Poaceae): a trans-Asian expedition in herbaria

Background and Aims

The hypothesis of an ancient introduction, i.e. archaeophyte origin, is one of the most challenging questions in phylogeography. Arundo donax (Poaceae) is currently considered to be one of the worst invasive species globally, but it has also been widely utilzed by man across Eurasia for millennia. Despite a lack of phylogenetic data, recent literature has often speculated on its introduction to the Mediterranean region.

Methods

This study tests the hypothesis of its ancient introduction from Asia to the Mediterranean by using plastid DNA sequencing and morphometric analysis on 127 herbarium specimens collected across sub-tropical Eurasia. In addition, a bioclimatic species distribution model calibrated on 1221 Mediterranean localities was used to identify similar ecological niches in Asia.

Key Results

Despite analysis of several plastid DNA hypervariable sites and the identification of 13 haplotypes, A. donax was represented by a single haplotype from the Mediterranean to the Middle East. This haplotype is shared with invasive samples worldwide, and its nearest phylogenetic relatives are located in the Middle East. Morphometric data characterized this invasive clone by a robust morphotype distinguishable from all other Asian samples. The ecological niche modelling designated the southern Caspian Sea, southern Iran and the Indus Valley as the most suitable regions of origin in Asia for the invasive clone of A. donax.

Conclusions

Using an integrative approach, an ancient dispersion of this robust, polyploid and non-fruiting clone is hypothesized from the Middle East to the west, leading to its invasion throughout the Mediterranean Basin.