A database of PCR primers for the chloroplast genomes of higher plants

BACKGROUND: Chloroplast genomes evolve slowly and many primers for PCR amplification and analysis of chloroplast sequences can be used across a wide array of genera. In some cases 'universal' primers have been designed for the purpose of working across species boundaries. However, the essential information on these primer sequences is scattered throughout the literature. RESULTS: A database is presented here which assembles published primer information for chloroplast DNA. Additional primers were designed to fill gaps where little or no primer information could be found. Amplicons are either the genes themselves (typically useful in studies of sequence variation in higher-order phylogeny) or they are spacers, introns, and intergenic regions (for studies of phylogeographic patterns within and among species). The current list of 'generic' primers consists of more than 700 sequences. Wherever possible, we give the locations of the primers in the thirteen fully sequenced chloroplast genomes (Nicotiana tabacum, Atropa belladonna, Spinacia oleracea, Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Pinus thunbergii, Marchantia polymorpha, Zea mays, Oenothera elata, Acorus calamus, Eucalyptus globulus, Medicago trunculata). CONCLUSION: The database described here is designed to serve as a resource for researchers who are venturing into the study of poorly described chloroplast genomes, whether for large- or small-scale DNA sequencing projects, to study molecular variation or to investigate chloroplast evolution

Epigenetic diversity of clonal white poplar (<i>Populus alba</i> L.) populations: could methylation support the success of vegetative reproduction strategy?

The widespread poplar populations of Sardinia are vegetatively propagated and live in different natural environments forming large monoclonal stands. The main goals of the present study were: i) to investigate/measure the epigenetic diversity of the poplar populations by determining their DNA methylation status; ii) to assess if and how methylation status influences population clustering; iii) to shed light on the changes that occur in the epigenome of ramets of the same poplar clone. To these purposes, 83 white poplar trees were sampled at different locations on the island of Sardinia. Methylation sensitive amplified polymorphism analysis was carried out on the genomic DNA extracted from leaves at the same juvenile stage. The study showed that the genetic biodiversity of poplars is quite limited but it is counterbalanced by epigenetic inter-population molecular variability. The comparison between MspI and HpaII DNA fragmentation profiles revealed that environmental conditions strongly influence hemi-methylation of the inner cytosine. The variable epigenetic status of Sardinian white poplars revealed a decreased number of population clusters. Landscape genetics analyses clearly demonstrated that ramets of the same clone were differentially methylated in relation to their geographic position. Therefore, our data support the notion that studies on plant biodiversity should no longer be restricted to genetic aspects, especially in the case of vegetatively propagated plant species

Back to black: a mineralogical and chemical characterisation of Atticising fourth century BCE black gloss ware

Most previous studies on Attic black gloss technology focused on productions from Greece, especially Athens. However, the black gloss technique constitutes the most widespread decoration practice across the Mediterranean from the Archaic to the Hellenistic periods. Focusing on both Attic and Atticising black gloss productions from sites in Sicily and Asia Minor, our work aims to shed new light on the technology of this decoration and its transmission throughout the Mediterranean during the fourth century BCE. Additionally, to investigate the technological relationship between black and the less common intentional red gloss decorations, a selection of bichrome black-and-red and red gloss vessels were included in this study. For this purpose, we applied an integrated analytical approach, aiming to characterise both the chemistry and the mineralogy of archaeological black and red gloss decorations. This approach includes ceramic petrography, pXRF, µ-XRD2, and SEM-EDS. Specimens from the fourth century BCE from Manfria (chora of Gela), Iasos (Caria), and Priene (Ionia) were analysed. These assemblages reflect various production groups identified by the chemical and petrographic analyses of the ceramic bodies. The µ-XRD2 and SEM-EDS measurements of the gloss show a certain degree of mineralogical and chemical variability that does not necessarily correlate with the recognised production groups but, rather, reflects different technological practices. Despite this variability, the results suggest that the various gloss productions were produced with a very similar technological process and offer new insights into the mechanisms through which the black gloss technique diffused throughout the Mediterranean

An interdisciplinary approach to the study of kiln firing: a case study from the Campus Galli open-air museum (southern Germany)

Pottery kilns are a common feature in the archaeological record of different periods. However, these pyrotechnological installations are still seldom the target of interdisciplinary investigations. To fill this gap in our knowledge, an updraft kiln firing experiment was run at the Campus Galli open-air museum (southern Germany) by a team consisting of experimental archaeologists, material scientists, geoarchaeologists, and palaeobotanists. The entire process from the preparation of the raw materials to the firing and opening of the kiln was carefully recorded with a particular focus on the study of the raw materials used for pottery making, as well as on fuel usage. The temperatures were monitored by thermocouples placed at different positions in the combustion and firing chambers. In addition, thermocouples were installed within the kiln wall to measure the temperature distribution inside the structure itself. Unfired raw materials as well as controlled and experimentally thermally altered ceramic samples were then characterised with an integrated analysis including ceramic petrography, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and portable X-ray fluorescence (pXRF). Our work provides data about mineralogical and microstructural developments in both pottery kiln structures and the ceramics produced in this type of installations. This is helpful to discuss the limits and potential of various scientific analyses commonly used in ancient ceramic pyrotechnological studies. Overall, our work contributes to a better understanding of updraft kiln technology and offers guidelines on how to address the study of this type of pyrotechnological installations using interdisciplinary research strategies

An interdisciplinary approach to the study of kiln firing: a case study from the Campus Galli open-air museum (southern Germany)

Pottery kilns are a common feature in the archaeological record of different periods. However, these pyrotechnological installations are still seldom the target of interdisciplinary investigations. To fill this gap in our knowledge, an updraft kiln firing experiment was run at the Campus Galli open-air museum (southern Germany) by a team consisting of experimental archaeologists, material scientists, geoarchaeologists, and palaeobotanists. The entire process from the preparation of the raw materials to the firing and opening of the kiln was carefully recorded with a particular focus on the study of the raw materials used for pottery making, as well as on fuel usage. The temperatures were monitored by thermocouples placed at different positions in the combustion and firing chambers. In addition, thermocouples were installed within the kiln wall to measure the temperature distribution inside the structure itself. Unfired raw materials as well as controlled and experimentally thermally altered ceramic samples were then characterised with an integrated analysis including ceramic petrography, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and portable X-ray fluorescence (pXRF). Our work provides data about mineralogical and microstructural developments in both pottery kiln structures and the ceramics produced in this type of installations. This is helpful to discuss the limits and potential of various scientific analyses commonly used in ancient ceramic pyrotechnological studies. Overall, our work contributes to a better understanding of updraft kiln technology and offers guidelines on how to address the study of this type of pyrotechnological installations using interdisciplinary research strategies

Forest genetic resources strategy for Europe

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Risks, benefits, and knowledge gaps of non-native tree species in Europe

Changing ecosystem conditions and diverse socio-economical events have contributed to an ingrained presence of non-native tree species (NNTs) in the natural and cultural European landscapes. Recent research endeavors have focused on different aspects of NNTs such as legislation, benefits, and risks for forestry, emphasizing that large knowledge gaps remain. As an attempt to fulfill part of these gaps, within the PEN-CAFoRR COST Action (CA19128) network, we established an open-access questionnaire that allows both academic experts and practitioners to provide information regarding NNTs from 20 European countries. Then, we integrated the data originating from the questionnaire, related to the country-based assessment of both peer-reviewed and grey literature, with information from available datasets (EUFORGEN and EU-Forest), which gave the main structure to the study and led to a mixed approach review. Finally, our study provided important insights into the current state of knowledge regarding NNTs. In particular, we highlighted NNTs that have shown to be less commonly addressed in research, raising caution about those characterized by an invasive behavior and used for specific purposes (e.g., wood production, soil recultivation, afforestation, and reforestation). NNTs were especially explored in the context of resilient and adaptive forest management. Moreover, we emphasized the assisted and natural northward migration of NNTs as another underscored pressing issue, which needs to be addressed by joint efforts, especially in the context of the hybridization potential. This study represents an additional effort toward the knowledge enhancement of the NNTs situation in Europe, aiming for a continuously active common source deriving from interprofessional collaboration.info:eu-repo/semantics/publishedVersio

Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree

Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of ‘hard selective sweeps’ vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees

DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird

© 2017 De Paoli-Iseppi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Most seabirds do not have any outward identifiers of their chronological age, so estimation of seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular age biomarker to estimate age in short-tailed shearwaters (Ardenna tenuirostris). We quantified DNA methylation in several A. tenuirostris genes that have shown age-related methylation changes in mammals. In birds ranging from chicks to 21 years of age, bisulphite treated blood and feather DNA was sequenced and methylation levels analysed in 67 CpG sites in 13 target gene regions. From blood samples, five of the top relationships with age were identified in KCNC3 loci (CpG66: R2 = 0.325, p = 0.019). In feather samples ELOVL2 (CpG42: R2 = 0.285, p = 0.00048) and EDARADD (CpG46: R2 = 0.168, p = 0.0067) were also weakly correlated with age. However, the majority of markers had no clear association with age (of 131 comparisons only 12 had a p-value &lt; 0.05) and statistical analysis using a penalised lasso approach did not produce an accurate ageing model. Our data indicate that some age-related signatures identified in orthologous mammalian genes are not conserved in the long-lived short tailed shearwater. Alternative molecular approaches will be required to identify a reliable biomarker of chronological age in these seabirds