Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene

Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.

Flexural anisotropy of rift-sawn softwood boards induced by the end-grain orientation

Inspired by the use of rift-sawn softwood board for covering curved surfaces in Kokerabuki, a traditional Japanese roofing method, we investigated the flexural anisotropy of wood caused by its end-grain orientation. We measured the flexural displacement of softwood species, Chamaecyparis obtusa and Cryptomeria japonica, and hardwood species, Populus suaveolens and Cerasus serrulata. For the softwood species, this was approximately five times longer for the rift-sawn specimens than for the other grain patterns. Using the replica method to measure the softwood tracheid deformation with different flexural displacements, we confirmed the different deformation mechanisms of the tracheid in the flat- and quarter-sawn specimens, and rift-sawn specimens. In the flat- and quarter-sawn woods, on-axis loading was generated, in which the stress was concentrated on the radial and tangential cell walls parallel to the direction of tension or compression. By contrast, in the rift-sawn wood, off-axis loading was generated, in which the stress was evenly distributed throughout the corner cell walls without the wall directly resisting the tensile and compressive forces. We also concluded that the tapered shape of the tracheid walls contributes to the excellent flexibility of rift-sawn softwood.

Using U-Net-Like Deep Convolutional Neural Networks for Precise Tree Recognition in Very High Resolution RGB (Red, Green, Blue) Satellite Images

Very high resolution satellite imageries provide an excellent foundation for precise mapping of plant communities and even single plants. We aim to perform individual tree recognition on the basis of very high resolution RGB (red, green, blue) satellite images using deep learning approaches for northern temperate mixed forests in the Primorsky Region of the Russian Far East. We used a pansharpened satellite RGB image by GeoEye-1 with a spatial resolution of 0.46 m/pixel, obtained in late April 2019. We parametrized the standard U-Net convolutional neural network (CNN) and trained it in manually delineated satellite images to solve the satellite image segmentation problem. For comparison purposes, we also applied standard pixel-based classification algorithms, such as random forest, k-nearest neighbor classifier, naive Bayes classifier, and quadratic discrimination. Pattern-specific features based on grey level co-occurrence matrices (GLCM) were computed to improve the recognition ability of standard machine learning methods. The U-Net-like CNN allowed us to obtain precise recognition of Mongolian poplar (Populus suaveolens Fisch. ex Loudon s.l.) and evergreen coniferous trees (Abies holophylla Maxim., Pinus koraiensis Siebold & Zucc.). We were able to distinguish species belonging to either poplar or coniferous groups but were unable to separate species within the same group (i.e. A. holophylla and P. koraiensis were not distinguishable). The accuracy of recognition was estimated by several metrics and exceeded values obtained for standard machine learning approaches. In contrast to pixel-based recognition algorithms, the U-Net-like CNN does not lead to an increase in false-positive decisions when facing green-colored objects that are similar to trees. By means of U-Net-like CNN, we obtained a mean accuracy score of up to 0.96 in our computational experiments. The U-Net-like CNN recognizes tree crowns not as a set of pixels with known RGB intensities but as spatial objects with a specific geometry and pattern. This CNN’s specific feature excludes misclassifications related to objects of similar colors as objects of interest. We highlight that utilization of satellite images obtained within the suitable phenological season is of high importance for successful tree recognition. The suitability of the phenological season is conceptualized as a group of conditions providing highlighting objects of interest over other components of vegetation cover. In our case, the use of satellite images captured in mid-spring allowed us to recognize evergreen fir and pine trees as the first class of objects (“conifers”) and poplars as the second class, which were in a leafless state among other deciduous tree species.

ELEMENTAL COMPOSITION OF THE BARK OF CERTAIN SPECIES AND HYBRIDS OF BALSAMIC POPLAR CULTIVATED IN UKRAINE

Keywords: elemental composition, bark, family willow, balsamic poplar. By the method atomic-emission spectrography with photographic registration the content of 19 elements in the barks Populus balsamifera L., Populus laurifolia L., Populus trichocarpa Torr. Gray., Populus suaveolens Fisch., Populus × berolinensis Dipp., which are cultivated in Ukraine, was determine. Raw materials for research were harvested from growing in the botanical garden of V.N. Karazin Kharciv National University (50°01′46″ N 36°14′02″ E.) in April 2019. As the content of the element in the bark decreases, they can be placed in the following rows: Populus balsamifera L.: Са<Mg<Si<P<K<Fe<Al<Na = Zn<Mn<Cu<Mo=Ni=Sr; Populus laurifolia L.: Ca<Si<Mg<P<Na<K<Fe = Zn<Al<Mn<Sr<Ni<Cu<Mo; Populus trichocarpa Torr. Gray.: Са<Mg<Si<P<K<Na<Fe = Al<Mn<Zn<Ni<Cu<Sr<Mo; Populus suaveolens Fisch.: Са<Mg<P<Si<Na<K<Al<Fe <Zn<Mn<Cu<Sr<Ni<Mo; Populus × berolinensis Dipp.: Са<Mg<Si<P<K<Fe = Al<Zn<Na<Mn<Cu<Ni=Sr=Mo. The content of Са (837,0 – 1225,0 mg/100 g), Мg (122,0 – 260,0 mg/100g), Si (130,0 – 230,0 mg/100 g) in the barks of all view is dominate. The highest content of elements defined in the Populus laurifolia L. (2324,4 mg /100 g) and the lowest in the bark of Populus ×berolinensis Dipp. (1623,4 mg/100 g). In terms of the content of heavy metals, the raw material meets the requirements of the Ukrainian State Pharmacopoeia. The obtained data make it possible to predict certain types of pharmacological activity of extracts and substances obtained from poplar bark and will be used in the development of quality control methods for raw materials.

Complex evaluation of the modern atmospheric air of city ecosystems

The results of studies of the chemical composition of atmospheric air showed that the concentration of ammonia (0.2520 mg/m3), nitrogen dioxide (0.3942 mg/m3) and hydrogen sulfide (0.0269 mg/m3) exceeded the MPC requirements. The seasonal dynamics of the spread of aerogenic pollutants revealed a decrease in NO, NO2, H2S, SO2 from winter to the spring-summer season. However, the content of such pollutants as NH3, CO and dust increased significantly in summer to 0.0816, 3.7140 and 0.0289 mg/m3 respectively. During bio-indication of 363 trees only 4 species of the 16 studied ones were characterized as healthy (K<1.5). The overall level of attenuation was 2.16 (“weakened forest”). Evaluation of the fluctuating asymmetry showed high resistance of the maple (Acer Platanoides) to environmental pollution (the level of asymmetry in the transport zone was 0.039 against 0.077–0.078 in the silver birch (Betula pendula) and the fragrant poplar (Populus suaveolens). The high level of anthropogenic pollution in the transport zones of the city adversely affected roadside biotopes. It has been proven that roadside phytocenosis is significantly sparse and the population density drops sharply by 50–100 %, compared to cleaner functional areas. The results of lichenoid indication showed that in most of the sites studied, the air was highly polluted (pollution class 1) and the concentration of SO2 was 0.10–0.30 mg/m3.