A Multiscale Vibrational Spectroscopic Approach for Identification and Biochemical Characterization of Pollen.

BACKGROUND: Analysis of pollen grains reveals valuable information on biology, ecology, forensics, climate change, insect migration, food sources and aeroallergens. Vibrational (infrared and Raman) spectroscopies offer chemical characterization of pollen via identifiable spectral features without any sample pretreatment. We have compared the level of chemical information that can be obtained by different multiscale vibrational spectroscopic techniques. METHODOLOGY: Pollen from 15 different species of Pinales (conifers) were measured by seven infrared and Raman methodologies. In order to obtain infrared spectra, both reflectance and transmission measurements were performed on ground and intact pollen grains (bulk measurements), in addition, infrared spectra were obtained by microspectroscopy of multigrain and single pollen grain measurements. For Raman microspectroscopy measurements, spectra were obtained from the same pollen grains by focusing two different substructures of pollen grain. The spectral data from the seven methodologies were integrated into one data model by the Consensus Principal Component Analysis, in order to obtain the relations between the molecular signatures traced by different techniques. RESULTS: The vibrational spectroscopy enabled biochemical characterization of pollen and detection of phylogenetic variation. The spectral differences were clearly connected to specific chemical constituents, such as lipids, carbohydrates, carotenoids and sporopollenins. The extensive differences between pollen of Cedrus and the rest of Pinaceae family were unambiguously connected with molecular composition of sporopollenins in pollen grain wall, while pollen of Picea has apparently higher concentration of carotenoids than the rest of the family. It is shown that vibrational methodologies have great potential for systematic collection of data on ecosystems and that the obtained phylogenetic variation can be well explained by the biochemical composition of pollen. Out of the seven tested methodologies, the best taxonomical differentiation of pollen was obtained by infrared measurements on bulk samples, as well as by Raman microspectroscopy measurements of the corpus region of the pollen grain. Raman microspectroscopy measurements indicate that measurement area, as well as the depth of focus, can have crucial influence on the obtained data.

Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq.

We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of Cedrus atlantica, a conifer tree species. With each method, Illumina(®) reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script to estimate the ascertainment bias in SNP detection considering the pooling and sampling effects on the probability of not detecting an existing polymorphism. Gene Ontology (GO) and transposable element (TE) search analyses were applied to both data sets. The RADseq and the mRNAseq assemblies represented 0.1% and 0.6% of the genome, respectively. Genome complexity reduction resulted in 17% of the RADseq contigs potentially coding for proteins. This rate was doubled in the mRNAseq data set, suggesting that RADseq also explores noncoding low-repeat regions. The two methods gave very similar GO-slim profiles. As expected, the two assemblies were poor in TE-like sequences (<4% of contigs length). We identified 17,348 single nucleotide polymorphisms (SNPs) in the RADseq data set and 5,714 simple sequence repeats (SSRs) in the transcriptome. A subset of 282 SNPs was validated using the Fluidigm genotyping technology, giving a conversion rate of 50.4%, falling within the expected range for conifers. Increasing sample size had the greatest effect for ascertainment bias reduction. These results validated the utility of the RADseq approach for highly complex genomes such as conifers.

Chemical variability of the wood essential oil of Cedrus atlantica Manetti from Corsica.

The composition of 48 samples of essential oil isolated from the wood of Cedrus atlantica growing in Corsica was investigated by GC (in combination with retention indices), GC/MS, and (13) C-NMR. Twenty-three compounds accounting for 73.9-96.0% of the oil composition were identified. The oils consisted mainly of monoterpene hydrocarbons and sesquiterpenes, in particular α-pinene (5; up to 79.4%), himachalol (4; up to 66.2%), ß-pinene (up to 21.4%), ß-himachalene (2; up to 19.3%), γ-himachalene (3; up to 11.0%), and α-himachalene (1; up to 10.9%). The 48 oil compositions were submitted to k-means partitioning and principal-component analysis, which allowed the distinction of two groups within the oil samples. The composition of Group I (44% of the samples) was dominated by 5, while the samples of Group II (56% of the samples) contained mainly 4.

Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies.

As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

Effective number of clones in seed orchards of Cedrus libani A. Rich.

Numbers of clone and ramet/clone were studied and discussed based on effective number of clones and relative effective number of clones in seed orchards of Taurus cedar (Cedrus libani A. Rich.). While, seed orchards had similar number of clones (15, 30 and 33), there were large differences for number of graft/clone within and among orchards. Number of ramets per clone varied between 4 and 43 in an orchard and between 4 and 106 in all orchards considered. Effective number of clones ranged from 24.6-31.4 and relative effective number from 0.82 to 0.99. The results of the study showed that ramet number had moderate variation among clones. It was important that establishment and thinning of seed orchards and estimation of gene diversity in seed orchard crop.

Drought effects on hydraulic conductivity and xylem vulnerability to embolism in diverse species and provenances of Mediterranean cedars.

We studied hydraulic traits of young plants of the Mediterranean cedar species Cedrus atlantica (Endl.) G. Manetti ex Carrière (Luberon, France), C. brevifolia (Hook. f.) Henry (Cyprus), C. libani A. Rich (Hadeth El Jebbe, Lebanon) and C. libani (Armut Alani, Turkey). With an optimum water supply, no major differences were observed among species or provenances in either stem hydraulic conductivity (Ks) or leaf specific conductivity (Kl) measured on the main shoot. A moderate soil drought applied for 10 weeks induced marked acclimation through a reduction in Ks, particularly in the Lebanese provenance of C. libani, and a decrease in tracheid lumen size in all species. Cedrus atlantica, which had the smallest tracheids, was the species most vulnerable to embolism: a 50% loss in hydraulic conductivity (PsiPLC50) occurred at a water potential of -4.4 MPa in the well-watered treatment, and at -6.0 MPa in the moderate drought treatment. In the other species, PsiPLC50 was unaffected by moderate soil drought, and only declined sharply at water potentials between -6.4 and -7.5 MPa in both irrigation treatments. During severe drought, Ks of twigs and stomatal conductance (g(s)) were measured simultaneously as leaf water potential declined. For all species, lower vulnerability to embolism based on loss of Ks was recorded on current-year twigs. The threshold for stomatal closure (10% of maximum g(s)) was reached at a predawn water potential (Psi(pd)) of -2.5 MPa in C. atlantica (Luberon) and at -3.1 MPa in C. libani (Lebanon), whereas the other provenance and species had intermediate Psi(pd) values. Cedrus brevifolia, with a Psi(pd) (-3.0 MPa) close to that of C. libani (Lebanon), had the highest stomatal conductance of the study species. The importance of a margin of safety between water potential causing stomatal closure and that causing xylem embolism induction is discussed.

Gene flow among different taxonomic units: evidence from nuclear and cytoplasmic markers in Cedrus plantation forests.

Hybridization and introgression are important natural evolutionary processes that can be successfully investigated using molecular markers and open- and controlled-pollinated progeny. In this study, we collected open-pollinated seeds from Cedrus atlantica, Cedrus libani and C. libani x C. atlantica hybrids from three French-plantation forests. We also used pollen from C. libani and Cedrus brevifolia to pollinate C. atlantica trees. The progeny were analyzed using three different types of molecular markers: RAPDs, AFLPs and cpSSRs. Chloroplast DNA was found to be paternally inherited in Cedrus from the progeny of controlled-crosses. Heteroplasmy, although possible, could not be undoubtedly detected. There was no indication of strong reproductive isolating barriers among the three Mediterranean Cedrus taxa. Gene flow between C. atlantica and C. libani accounted for 67 to 81% of viable open-pollinated seedlings in two plantation forests. We propose that Mediterranean Cedrus taxa should be considered as units of a single collective species comprising two regional groups, North Africa and the Middle East. We recommend the use of cpSSRs for monitoring gene flow between taxa in plantation forests, especially in areas where garden specimens of one species are planted in the vicinity of selected seed-stands and gene-conservation reserves of another species.

Taxonomy of gymnospermae: multivariate analyses of leaf fatty acid composition.

The fatty acid composition of photosynthetic tissues from 137 species of gymnosperms belonging to 14 families was determined by gas chromatography. Statistical analysis clearly discriminated four groups. Ginkgoaceae, Cycadaceae, Stangeriaceae, Zamiaceae, Sciadopityaceae, Podocarpaceae, Cephalotaxaceae, Taxaceae, Ephedraceae and Welwitschiaceae are in the first group, while Cupressaceae and Araucariaceae are mainly in the second one. The third and the fourth groups composed of Pinaceae species are characterized by the genera Larix, and Abies and Cedrus, respectively. Principal component and discriminant analyses and divisive hierarchical clustering analysis of the 43 Pinaceae species were also performed. A clear-cut separation of the genera Abies, Larix, and Cedrus from the other Pinaceae was evidenced. In addition, a mass analysis of the two main chloroplastic lipids from 14 gymnosperms was performed. The results point to a great originality in gymnosperms since in several species and contrary to the angiosperms, the amount of digalactosyldiacylglycerol exceeds that of monogalactosyldiacylglycerol.