Experimental quantification of pollen with DNA metabarcoding using ITS1 and trnL.

Although the use of metabarcoding to identify taxa in DNA mixtures is widely approved, its reliability in quantifying taxon abundance is still the subject of debate. In this study we investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high-throughput sequence reads and how the relationship was affected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have different characteristics. We found a significant positive relationship between the number of DNA sequences and the number of pollen grains in the mock solutions. However, better relationships were obtained with light microscopy as a pollen grain counting method compared with flow cytometry, with the chloroplastic trnL marker compared with ribosomal ITS1 and with 30 when compared with 25 or 35 PCR cycles. We provide a list of recommendations to improve pollen quantification.

Phenotypic Trait Variation as a Response to Altitude-Related Constraints in Arabidopsis Populations.

Natural variations help in identifying genetic mechanisms of morphologically and developmentally complex traits. Mountainous habitats provide an altitudinal gradient where one species encounters different abiotic conditions. We report the study of 341 individuals of Arabidopsis thaliana derived from 30 natural populations not belonging to the 1001 genomes, collected at increasing altitudes, between 200 and 1800 m in the Pyrenees. Class III peroxidases and ribosomal RNA sequences were used as markers to determine the putative genetic relationships among these populations along their altitudinal gradient. Using Bayesian-based statistics and phylogenetic analyses, these Pyrenean populations appear with significant divergence from the other regional accessions from 1001 genome (i.e., from north Spain or south France). Individuals of these populations exhibited varying phenotypic changes, when grown at sub-optimal temperature (22 vs. 15°C). These phenotypic variations under controlled conditions reflected intraspecific morphological variations. This study could bring new information regarding the west European population structure of A. thaliana and its phenotypic variations at different temperatures. The integrative analysis combining genetic, phenotypic variation and environmental datasets is used to analyze the acclimation of population in response to temperature changes. Regarding their geographical proximity and environmental diversity, these populations represent a tool of choice for studying plant response to temperature variation. HIGHLIGHTS: -Studying the natural diversity of A. thaliana in the Pyrenees mountains helps to understand European population structure and to evaluate the phenotypic trait variation in response to climate change.

Pollinator specialization increases with a decrease in a mass-flowering plant in networks inferred from DNA metabarcoding.

How native mass-flowering plants affect the specialization of insects at individual and species levels and the consequences for pollination networks have received much less attention than for mass-flowering crops or alien species and basically remain unexplored.Using existing DNA metabarcoding data on the pollen loads of 402 flower-visiting insects, we assessed the effects of a native mass-flowering plant of high reward quality, the shrub Rhododendron ferrugineum, on pollination networks by investigating: (a) the food niches of individual pollinators and pollinator species and (b) the structure of individual and species networks in subalpine heathland patches with extremely contrasted densities of R. ferrugineum.Relative to its high abundance in high-density patches, the shrub was greatly underrepresented and did not dominate individual's or species' generalized networks, rather individual and species specialization increased with a decrease in R. ferrugineum density. Furthermore, individuals of the more generalist dipteran Empididae species tended to extend exclusive interactions with rare plant species in low-density networks. The same trend was observed in the more specialist Apidea but toward rare species in high-density networks. Our results reveal a quite paradoxical view of pollination and a functional complementarity within networks. Niche and network indices mostly based on the occurrence of links showed that individual pollinators and pollinator species and networks were highly generalized, whereas indices of link strength revealed that species and above all individuals behave as quite strict specialists. Synthesis. Our study provides insights into the status of a native mass-flowering plant in individual's and insect species' food niches and pollination networks. It revealed that a generalist pollinator species can be highly specialized at the individual level and how rare plant species coexisting with mass-flowering plants may nevertheless be visited.

Selection and gene flow shape genomic islands that control floral guides.

Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightly-linked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding "sea," making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.

DNA metabarcoding data unveils invisible pollination networks.

Animal pollination, essential for both ecological services and ecosystem functioning, is threatened by ongoing global changes. New methodologies to decipher their effects on pollinator composition to ecosystem health are urgently required. We compare the main structural parameters of pollination networks based on DNA metabarcoding data with networks based on direct observations of insect visits to plants at three resolution levels. By detecting numerous additional hidden interactions, metabarcoding data largely alters the properties of the pollination networks compared to visit surveys. Molecular data shows that pollinators are much more generalist than expected from visit surveys. However, pollinator species were composed of relatively specialized individuals and formed functional groups highly specialized upon floral morphs. We discuss pros and cons of metabarcoding data relative to data obtained from traditional methods and their potential contribution to both current and future research. This molecular method seems a very promising avenue to address many outstanding scientific issues at a resolution level which remains unattained to date; especially for those studies requiring pollinator and plant community investigations over macro-ecological scales.

Using metabarcoding to reveal and quantify plant-pollinator interactions.

Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.

The evolutionary history of Antirrhinum in the Pyrenees inferred from phylogeographic analyses.

BACKGROUND: The origin and colonisation history after the Quaternary ice ages remain largely unresolved for many plant lineages, mainly owing to a lack of fine-scale studies. Here, we present a molecular phylogeny and a phylogeographic analysis of Antirrhinum, an important model system in plant biology, in the Pyrenees range. Our goal was to reconstruct the evolutionary and colonisation history of four taxa endemic to this region (A. majus subsp. majus, A. majus. subsp. striatum, A. molle, and A. sempervirens) by using a dense sampling strategy, with a total of 452 individuals from 99 populations whose collective distribution spans nearly the entirety of the Pyrenees and adjacent mountains. RESULTS: Phylogenetic and phylogeographic analyses of the sequences of two plastid (trnS-trnG and trnK-matK) regions revealed the following: (i) historical relationship between the Pyrenees and Iberia (but not with the Alps); (ii) the long persistence of populations in the Pyrenees, at least since the Late Pleistocene; (iii) three different colonisation histories for populations from the Western, Central, and Eastern Pyrenees; (iv) the deep phylogeographic separation of the eastern and western populations; and (v) the colonisation of southern France from the Eastern Pyrenees. CONCLUSIONS: The present study underlines the enormous influence of the glacial history of the mountain ranges on the current configuration of intra- and inter-specific genetic diversity in Antirrhinum, as well as the importance of periglacial areas for the survival of species during glacial periods of the Quaternary.

Optimized nutrient medium for galanthamine production in Leucojum aestivum L. in vitro shoot system.

The common effect of NH4+, NO3-, KH2PO4 and sucrose on the biosynthesis of galanthamine by a Leucojum aestivum shoot culture was studied. Polynominal regression models were elaborated for the description of the galanthamine biosynthesis as a consequence of variation of the investigated variables (NH4+ between 0.20 and 0.54 g/L; NO3- between 1.44 and 3.44 g/L; KH2PO4 between 0.10 and 0.24 g/L, and sucrose between 30.00 and 60.00 g/L). Optimization procedures allowed us to establish the optimal concentrations of the investigated variables and to propose the modified MS nutrient medium, with 4.50 g/L KNO3, 0.89 g/L NH4NO3, 1.25 g/L (NH4)2SO4, 0.10 g/L KH2PO4 and 60 g/L sucrose, for the galanthamine production by a Leucojum aestivum shoot culture. The proposed modified MS medium provided considerable increase of both the production yield and the relative content of the target alkaloid in the alkaloid mixture.

Alkaloid synthesis and accumulation in Leucojum aestivum in vitro cultures.

The alkaloids of intact plants, calli and shoot-clump cultures of L. aestivum were analyzed by GC-MS. Twenty-four alkaloids were detected. Calli appeared to produce sparse alkaloid profiles in stark contrast to shoot-clumps that had similar profiles to those of the intact plant. Seven shoot-clump strains produced galanthamine predominantly whereas another three were dominated by lycorine. Shoot-clump strains cultivated under light accumulated about two-times more galanthamine (an average of 74 microg/g of dry weight) than those cultivated in darkness (an average of 39 microg/g of dry weight). In comparison to intact plants, the shoot-clumps accumulated 5-times less galanthamine. The high variability of both the galanthamine content (67% and 75% of coefficient of variation under light and darkness conditions, respectively) and alkaloid patterns indicates that the shoot-clump cultures initiated from callus could be used as a tool for improvement of the in vitro cultures.

Influence of plant origin on propagation capacity and alkaloid biosynthesis during long-term in vitro cultivation of Leucojum aestivum L.

The investigation deals with in vitro clonal propagation of L. aestivum L. (summer snowflake), a threatened Amaryllidaceae plant species in Bulgaria used in the pharmaceutical industry as raw material for production of galanthamine-based medicines. Plants of known origin and with different alkaloid profile were taken from the living collection of the Institute of Botany, Sofia. Bulbs were used to initiate in vitro cultures and 24 clones were multiplied. The influence of the clone origin on the propagation coefficient, shoot and bulblet morphology, alkaloid profile and content of galanthamine, lycorine, and four related alkaloids was evaluated. Clones kept stable alkaloid profiles and for most of them, high regeneration rates were noted. Galanthamine content of some clones was commensurable with that of Bulgarian populations of L. aestivum of commercial importance. Five clones: four galanthamine-type and one lycorine-type were selected as promising for further investigation.

CGC-MS of alkaloids in Leucojum aestivum plants and their in vitro cultures.

Underivatised alkaloid mixtures extracted from intact plants and in vitro cultures of Leucojum aestivum (Amaryllidaceae) were investigated by capillary GC-MS. Excellent peak resolution for the alkaloids was exhibited and isomers of galanthamine and N-formylnorgalanthamine were well separated. Fourteen alkaloids of galanthamine, lycorine and crinane types were identified, 11 in the intact plants and eight in the in vitro cultures.