Two-dimensional gel electrophoresis as a taxonomic tool: Evidence from the centrospermae

Two-dimensional polyacrylamide gel (2-D PAGE) electrophoresis was appraised as an experimental technique for assessing systematic relationships among higher plants and to determine at which level in the taxonomic hierarchy this technique is most generally applicable. 2-D PAGE was performed on denatured extracts of mature leaves from 25 species representing five families of the order Centrospermae (Caryophyllales, Chenopodiales) in the Angiospermae as well as Welwitschia mirabilis (Gymnospermae). Cluster analysis of a 256 spot binary-coded data set derived from the computer-encoded spot patterns of the 25 species successfully separated taxa from the individual to the familial levels of the taxonomic hierarchy in accordance with traditional taxonomic delineations of the taxa.     

Flavonols and C-Glycosylflavonoids of the caryophyllales

A survey of 112 species of the Caryophyllales showed the presence of flavonols in all eleven families and of C-glycosylflavonoids in nine families, being absent from the Aizoaceae and Cactaceae. 18% of the species contained both classes of compound. C-glycosylflavonoids are reported for the first time in the Amaranthaceae, Basellaceae, Didieraceae, Nyctaginaceae, Phytolaccaceae, Portulacaceae and Molluginaceae. The Caryophyllaceae contained prodominantly C-glycosylflavonoids, suggesting they are the most advanced family in the order.     

New Caledonia: A Hot Spot for Valuable Chemodiversity Part 3: Santalales,Caryophyllales, and Asterids

The flora of New Caledonia encompasses more than 3000 plant species and an endemism of almost 80%. New Caledonia is even considered as one of the 34 ‘hot spots’ for biodiversity. Considering the current global loss of biodiversity and the fact that several drugs and pesticides become obsolete, there is an urgent need to increase sampling and research on new natural products. In this context, here, we reviewed the chemical knowledge available on New Caledonian native flora from economical perspectives. We expect that a better knowledge of the economic potential of plant chemistry will encourage the plantation of native plants for the development of a sustainable economy which will participate in the conservation of biodiversity. This review is divided into three parts, and the third part which is presented here summarizes the scientific literature related to the chemistry of endemic santalales, caryophyllales, and asterids. We show that the high rate of endemism is correlated with the originality of phytochemicals encountered in New Caledonian plants. A total of 176 original natural compounds have been identified from these plants, whereas many species have not been investigated so far. We also discuss the economic potential of plants and molecules with consideration of their medicinal and industrial perspectives. This review finally highlights several groups, such as Sapotaceae, that are unexplored in New Caledonia despite the high chemical interest in them. These plants are considered to have priority in future chemical investigations.     

Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0729-7) contains supplementary material, which is available to authorized users.     

Quantifying succulence: a rapid, physiologically meaningful metric of plant water storage

Quantification of succulence should ideally convey information about physiological function and yet also be straightforward to measure. While important aspects of succulence and its physiological consequences may be quantified using parameters derived from pressure-volume (P-V) curves, this technique applied to succulent tissues is difficult, time consuming and generally not suitable for large comparative datasets. We performed P-V curves on leaves of 25 taxa from across Caryophyllales and compared the results with direct measures of saturated water content (SWC(meas) ), the ratio of water mass at full saturation to tissue dry mass, for the same taxa. SWC(meas) was significantly related to relative capacitance, the most physiologically relevant parameter describing tissue succulence. We developed a linear model describing SWC(meas) as a function of relative capacitance and leaf volume, which is also supported when accounting for the phylogenetic relationships among taxa. These results indicate that SWC(meas) is a suitable proxy for tissue succulence, and that both cellular properties and variation in gross morphology contribute towards a plant's relative water storage capacity. Quantifying SWC(meas) across many taxa showing variation in tissue succulence will provide a new avenue for exploring the evolutionary dynamics of this important ecological adaptation.     

Wood anatomy of Polygonaceae: analysis of a family with exceptional wood diversity

Quantitative and qualitative data are presented for woods of 30 species of woody Polygonaceae. Wood features that ally Polygonaceae with Plumbaginaceae include nonbordered perforation plates, storeying in narrow vessels and axial parenchyma, septate or nucleate fibres, vasicentric parenchyma, pith bundles that undergo secondary growth, silica bodies, and ability to form successive cambia. These features are consistent with pairing of Plumbaginaceae and Polygonaceae as sister families. Wood features that ally Polygonaceae with Rhabdodendraceae include nonbordered perforation plates, presence of vestured pits in vessels, presence of silica bodies and dark-staining compounds in ray cells, and ability to form successive cambia. Of the features listed above, nonbordered perforation plates and ability to form successive cambia may be symplesiomorphies basic to Caryophyllales sensu lato . The other features are more likely to be synapomorphies. Wood data thus support molecular cladograms that show the three families near the base of Caryophyllales s.l. Chambered crystals are common to three genera of the family and may indicate relationship. Ray histology suggests secondary woodiness in Antigonon, Atraphaxis, Bilderdykia, Dedeckera, Eriogonum, Harfordia, Muehlenbeckia, Polygonum , and Rumex . Other genera of the family show little or no evidence of secondary woodiness. Molecular data are needed to confirm this interpretation and to clarify the controversial systematic groupings within the family proposed by various authors. Vessel features of Polygonaceae (lumen diameter, element length, density, degree of grouping) show an extraordinary range from xeromorphy to mesomorphy, indicating that wood has played a key role in ecological and habital shifts within the family; the diversity in ecology and habit are correlated with quantitative wood data.  © 2003 The Linnean Society of London. Botanical Journal of the Linnean Society , 2003, 141 , 25−51.     

Crassulacean acid metabolism in the Basellaceae (Caryophyllales)

• C₄ and crassulacean acid metabolism (CAM) have evolved in the order Caryophyllales many times but neither C₄ nor CAM have been recorded for the Basellaceae, a small family in the CAM‐rich sub‐order Portulacineae.
• 24 h gas exchange and day–night changes in titratable acidity were measured in leaves of Anredera baselloides exposed to wet–dry–wet cycles.
• While net CO₂ uptake was restricted to the light period in well‐watered plants, net CO₂ fixation in the dark, accompanied by significant nocturnal increases in leaf acidity, developed in droughted plants. Plants reverted to solely C₃ photosynthesis upon rewatering.
• The reversible induction of nocturnal net CO₂ uptake by drought stress indicates that this species is able to exhibit CAM in a facultative manner. This is the first report of CAM in a member of the Basellaceae.

     

Molecular phylogenetics of Alternanthera (Gomphrenoideae,Amaranthaceae): resolving a complex taxonomic history caused by different interpretations of morphological characters in a lineage with C4 and C3–C4 intermediate species

Alternanthera (Amaranthaceae) is a diverse genus (80–200 species) largely restricted to the American Tropics. With Pedersenia and Tidestromia, it makes up the ‘Alternantheroid clade’ in Gomphrenoideae. Parsimony and Bayesian analyses of nucleotide sequences of nuclear (ITS) and plastid (rpl16, trnL‐F) and morphological characters identify that the capitate stigma of Alternanthera is a synapomorpy within the Alternantheroids. Within Alternanthera, two major clades were resolved, both of which were marked by otherwise homoplasious characters of the gynoecium: Clade A [99% jackknife (JK); 1.0 posterior probability (PP)] with nine species and Clade B (60% JK; 0.98 PP) with 22 species. Four subclades (B1–B4), strongly supported statistically, were identified in Clade B. Previous subgeneric classifications of Alternanthera appear artificial in light of our new molecular phylogenetic analyses. Most major lineages are congruently resolved by nuclear and plastid data but some incongruence between the nrITS and plastid phylogenetic trees suggests hybridization may have played a role in the rampant speciation in Alternanthera. Whereas C₄ photosynthesis appears to have evolved in a single clade, the position of A. littoralis var. maritima (C₃) in this clade may be explained by hybrid speciation rather than a reversal from C₄ to C₃. All C₃–C₄ intermediates belong to a different clade that also contains C₃ species, but species limits, including the widely studied A. tenella, are unclear. The clade including A. tenella and A. halimifolia contains most of the species endemic to the Galápagos whereas A. nesiotes, also endemic to the islands, is nested among widespread American taxa. This suggests that the Galápagos radiation of Alternanthera may have arisen from at least two independent colonization events followed by a subsequent radiation in the former lineage. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 493–517.     

Molecular phylogenetic analysis of Arenaria (Caryophyllaceae: tribe Arenarieae) and its allies inferred from nuclear DNA internal transcribed spacer and plastid DNA rps16 sequences

The systematics and phylogeny of the genus Arenaria and allied genera are unresolved. The use of morphological data has resulted in contradictory taxonomic concepts in the past due to their homoplastic nature. We present a phylogenetic analysis based on internal transcribed spacer (ITS) and rps16 sequence data of 140 (132 taxa) and 131 (120 taxa) accessions, respectively. Maximum parsimony and Bayesian analyses of each marker produced nearly congruent trees. Monophyly of Arenaria s.s. and Eremogone is confirmed here. Our results corroborate earlier results indicating that Arenaria subgenus Odontostemma is monophyletic, but outside the core group of Arenaria. Arenaria subgenus Solitaria is sister to Odontostemma and also not closely related to the latter; both of these subgenera are excluded from Arenaria and treated as distinct genera. The molecular data indicate that the ‘Arenaria s.s. clade’ consists of a few well‐supported subgroups and that the current subgeneric classification of the genus does not reflect evolutionary history. Arenaria subgenus Leiosperma is clearly monophyletic, but we reduce it to sectional level. Our molecular data show that the monotypic Arenaria subgenera Porphyrantha and Arenariastrum are nested in A. subgenus Arenaria, whereas subgenus Eremogoneastrum is included in Eremogone. None of the species‐rich sections in subgenus Arenaria is monophyletic. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 648–669.     

Wood and stem anatomy of woody Amaranthaceae s.s.: ecology, systematics and the problems of defining rays in dicotyledons

Wood and stem anatomy is studied for seven species of six genera (root anatomy also reported for one species) of Amaranthaceae s.s. Quantitative data on vessels correlate closely with relative xeromorphy of respective species, agreeing with values reported for dicotyledons without successive cambia in comparable habitats. Libriform fibre abundance increases and vessel diameter decreases as stems and roots of the annual Amaranthus caudatus mature. Long, thick-walled fibres in Bosea yervamora may be related to the upright nature of elongate semi-climbing stems. Non-bordered or minutely bordered perforation plates characterize Amaranthaceae, as they do most other Caryophyllales. Amaranthaceae have idioblastic cells containing druses, rhomboidal crystals or crystal sand: these forms intergrade and seem closely related. Rays are present in secondary xylem of the Amaranthaceae studied. Cells intermediate between ray cells and libriform fibres occur in Charpentiera elliptica . Degrees of diversity in rays and reports of raylessness in Amaranthaceae induce discussion of definition and identification of rays in dicotyledons; some sources recognize both rays and radial plates of conjunctive tissue in Amaranthaceae. The action of successive cambia is described: lateral meristem periclinal divisions produce secondary cortex externally, conjunctive tissue internally and yield vascular cambia as well. Vascular cambia produce secondary phloem and secondary xylem, in both ray and fascicular zones, as in a dicotyledon with a single cambium. Identification of meristem activity and appreciation of varied ray manifestations are essential in understanding the ontogeny of stems in Amaranthaceae (which have recently been united with Chenopodiaceae).  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 1–19.