This work is a long-term outcome of an international Ukrainian-Polish teamwork, aiming to assess the role of ancient settlements for steppe conservation and protection. The dataset contains ...georeferenced occurrences of vascular plant species on 18 ancient settlements (Lower Dnipro, southern Ukraine), collected during the 2015-2020 period. Additionally, to the total species list, the publication presents the taxonomic coverage (according to GBIF Backbone Taxonomy), the frequency classes of occurrences of the total taxa and the floristic differences amongst studied sites. The report also shows the high sozological value of the studied ancient settlements, the high levels of vascular plant species richness and the various means of the plant species protection (according to the Bern Convention, the Red Data Book of Ukraine and regional Red Lists).
This work provides the first occurrence dataset from ancient settlements in Ukraine. The dataset includes 3,210 occurrences of vascular plants recorded during the study period of 2015-2020 conducted in the Lower Dnipro region. As ancient settlements were generally considered as steppe refuges, great attention was paid to the native steppe species, as well as to the rare components of the flora. The dataset includes 1,525 occurrences of steppe species and 87 occurrences of rare species, respectively. The dataset could be useful for further research of ancient settlements` floristic richness, but also analyses and comparison with other objects of cultural origin (e.g. kurgans, hillforts, old cemeteries, forgotten parks, sacred groves etc.).
Key message
Extensive modulation of numerous
ARF
transcripts in the embryogenic culture of Arabidopsis indicates a substantial role of auxin signaling in the mechanism of somatic embryogenesis ...induction.
Somatic embryogenesis (SE) is induced by auxin in plants and auxin signaling is considered to play a key role in the molecular mechanism that controls the embryogenic transition of plant somatic cells. Accordingly, the expression of
AUXIN RESPONSE FACTOR
(
ARF
) genes in embryogenic culture of Arabidopsis was analyzed. The study revealed that 14 of the 22
ARFs
were transcribed during SE in Arabidopsis. RT-qPCR analysis indicated that the expression of six
ARF
s (
ARF5, ARF6, ARF8, ARF10, ARF16
, and
ARF17
) was significantly up-regulated, whereas five other genes (
ARF1, ARF2, ARF3, ARF11
, and
ARF18
) were substantially down-regulated in the SE-induced explants. The activity of
ARF
s during SE was also monitored with GFP reporter lines and the
ARF
s that were expressed in areas of the explants engaged in SE induction were detected. A functional test of
ARF
s transcribed during SE was performed and the embryogenic potential of the
arf
mutants and overexpressor lines was evaluated.
ARF
s with a significantly modulated expression during SE coupled with an impaired embryogenic response of the relevant mutant and/or overexpressor line, including
ARF1, ARF2, ARF3, ARF5, ARF6, ARF8
, and
ARF11
were indicated as possibly being involved in SE induction. The study provides evidence that embryogenic induction strongly depends on
ARFs
, which are key regulators of the auxin signaling. Some clues on the possible functions of the candidate
ARF
s, especially
ARF5
, in the mechanism of embryogenic transition are discussed. The results provide guidelines for further research on the auxin-related functional genomics of SE and the developmental plasticity of somatic cells.
Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant ...modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.
Abstract
For many years, research has been carried out with the aim of understanding the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is ...the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review summarizes over 30 years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, namely embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and, finally, all the genes under its direct control. In addition, information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years.
A review of the action of MP/ARF5 in auxin-dependent regulation of gene expression, its role in the plant developmental process, and available tools for molecular analysis.
Epigenetic processes including DNA methylation play a pivotal role in regulating the genes that control plant development. In contrast to
in planta
development, the contribution of DNA methylation to ...the morphogenic processes that are induced in vitro are much less recognised. Hence, in the present study, we analysed the impact of DNA methylation on somatic embryogenesis (SE) that was induced in Arabidopsis. The results demonstrated a decrease in the global DNA methylation level during SE that contrasted with the up-regulation of
MET1
and
CMT3
DNA methylases and the down-regulation of DNA demethylases (
ROS1, DME
and
DML2
). Hence, the global DNA methylation level appears not to correlate with the transcriptional activity of the genes encoding DNA methylases/demethylases, thereby implying the complexity of the regulatory mechanism that controls the DNA methylation status of the SE-epigenome. Moreover, distinct changes in the expression level of the SE-regulatory genes were indicated in the 5-AzaC-treated and DNA methylase mutant cultures. Accordingly, a significant repression of the
LEC2, LEC1
and
BBM
genes was found in the 5-AzaC-treated culture that was incapable of SE induction. In contrast, the distinct up-regulation of these genes was observed in the
drm1drm2
and
drm1drm2cmt3
mutant cultures with an improved embryogenic response. The modulated expression of DNA methylase genes and the significantly modified embryogenic response of the
met1
and
drm
mutants imply that both the maintenance and the de novo pathway of DNA methylation are engaged in the regulation of SE in Arabidopsis.
Polycyclic aromatic hydrocarbons (PAHs) and heavy metals are the two most important groups of pollutants associated with rail transport. Both have a serious negative impact on the natural ...environment, including human health and degradation of sensitive ecosystems. In our study, apart from qualitative and quantitative analysis of the main PAHs and heavy metals associated with rail, we tried to assess composition of specific compounds related to functional areas of railway infrastructure and to distinguish potential chemical markers which can be used for identification of pollution. Moreover, we evaluated the applicability of plants overgrowing railway infrastructure as bioindicators of rail-associated pollution. Though we confirmed that high amounts of PAHs and heavy metals in soil are characteristic for intensively used railway infrastructure, we found no typical pollution profiles for the differently used areas (i.e. platforms, sidings, cleaning bays). The major source of these contaminants is petroleum products used in conservation of railway infrastructure and rolling stock. As far as the use of plants overgrowing railway infrastructure as bioindicators of rail-associated pollution is concerned, it is rather limited, due to frequent application of herbicides for security and track stability reasons.
Main conclusion The ERF022 gene was found to affect embryogenic transition in somatic cells in Arabidopsis via the ethylene-related pathway. The study provides evidence that ERF022-LEC2 interaction ...is involved in the auxin-ethylene crosstalk that operates in somatic embryogenesis induction. The ERF022 gene of the ERF family was previously identified among the transcription factor genes that were differentially expressed in an embryogénie culture of Arabidopsis. A strong inhibition of the gene was found to be associated with the induction of somatic embryogenesis (SE) and an erfO22 mutant was indicated to display a substantially impaired capacity for SE. Therefore, the molecular function of ERF022 in the induction of SE was studied in the present work. A phenotype of an erf022 mutant was indicated as being related to an increased content of ethylene. The results further suggest that the ERF022 controls the genes that are involved in both the biosynthesis (ACS7) and signalling (ERF1, ETR1) of ethylene and indicate that the ERF022 is a new regulatory element in ethylene-related responses that negatively control the ethylene content and perception. It is proposed that the negative impact of ethylene on the induction of SE may result from a modulation of the auxin-related genes that control the embryogenic transition in somatic cells. Among them, the LEC2, which is a key regulator of the induction of SE through the stimulation of auxin synthesis, was possibly related to ERF022. The results of the study provide new hormone-related clues to define the genetic network that governs SE. A putative model of the regulatory pathway is proposed that is involved in the induction of SE in which the auxin-ethylene interactions are controlled by ERF022 and LEC2 and their targets.
The objective of this paper is to present the principle and results of selecting floristic parameters which best reflect the effects of different intensity and duration of anthropopressure within the ...borders of a large urban agglomeration (exemplified by Warsaw). Those parameters which in particular take into account such quantities as, for example, the percentage of kenophytes, therophytes-newcomers, permanently established synanthropes and so on, make it possible to assess the degree of advancement of flora synanthropization, including its temporal aspect. The results indicate that the selected parameters (especially their 3- or 6-component complexes) could also be of importance as indices of flora synanthropization in other cities, when floristic lists from different anthropopressure zones within each city are compared.
Heavy metal (As, Mn, Ni, Sn, Ti) concentrations were determined in soil and plant samples collected in different areas of the railway junction IÅawa GÅówna, Poland. Soil and plant samples were ...collected in four functional parts of the junction, i.e. the loading ramp, main track within the platform area, rolling stock cleaning bay and the railway siding. Four plant species occurring in relatively higher abundance were selected for heavy metals analysis, although in the loading ramp and platform areas only one species could be collected in the amount which makes chemical analysis possible. The selected species included three perennials (Daucus carota, Pastinaca sativa and Taraxacum officinale) and one annual plant (Sonchus oleraceus). The entire area of the railway junction showed elevated concentrations of heavy metals when compared to the control level. It was most pronounced for the platform area and railway siding. The concentration of arsenic, manganese and nickel in plants growing in these parts of the junction exceeded the toxic level. The highest contamination of soil and plants found in the platform area suggested advanced emission process of the analyzed metals from wheel and track abrasion. Literature review showed that the concentration of the investigated metals in soil was generally higher than that found in centers of cities and along traffic roads proving that the railway is an important linear source of soil contamination.
The dataset contains the records of vascular plant species occurrences and distribution on Ukrainian kurgans (burial mounds, barrows), located in various zones of steppe vegetation: desert steppe, ...grass steppe, herb-rich grass steppe and forest steppe. Much of the studied kurgans belongs to the territory historically known as the "Wild Fields". Besides the occurrence data, the publication presents a comparison of the floristic richness amongst five microhabitats distinguished on kurgans (top, northern slope, northern bottom, southern slope, and southern bottom) and amongst kurgans located in different steppe zones. The Original publication includes 721 species of vascular plants) within four vegetation zone (desert steppe, grass steppe, herb-rich grass steppe and forest steppe). The report shows also sozological value of kurgans in southern Ukraine, as they play a role of steppe habitat islands in a landscape almost completely transformed to arable land. The obtained flora inventory was analyzed in various aspects. This occurrence dataset is the first public record of species from kurgans in Ukraine.
This is the first occurrence dataset from kurgans in Ukraine. The dataset includes 28,456 occurrences of vascular plants recorded in the years 2004-2009 on Ukrainian kurgans. The dataset includes information about 1446 occurrences of rare species on kurgans (69 species). It contains information on the kurgan flora within four vegetation zone (desert steppe, grass steppe, herb-rich grass steppe and forest steppe) on the area ca. 32000 km
. Of the approximately 450 mounds visited, the ones with the best preserved vegetation cover were selected. For each of 106 investigated mounds, floristic lists from five microhabitats were compiled - 530 lists in total.
PDF
