Nikita Botanical Gardens Research Articles

First Report and Molecular Characterization of Umbra-like Virus on Ficus carica Caprifig Trees in Crimea.

Fig mosaic is the most serious viral disease affecting figs. A fig germplasm collection from the Nikita Botanical Garden on the Crimean Peninsula was surveyed for viruses using high-throughput sequencing and RT-PCR with primers specific to known fig viruses. Reads related to fig umbra-like virus (FULV) were generated in samples from Ficus carica caprifig (pollinator) trees of the cultivar Belle dure. F. carica trees of other cultivars, as well as F. afghanistanica, F. palmata, and F. virgata trees, tested negative for FULV. Near-complete genomes of five Crimean fig umbra-like virus (FULV-CR) isolates shared 99.4% to 99.9% identity and were most closely related (85.2% identity) to the Hawaiian FULV isolate Oahu1 (MW480892). Based on their genome structure and a phylogenetic analysis, the FULV-CR isolates were determined to be dicot-infecting Class 2 umbra-like viruses and seem to be highly divergent forms of the same virus found recently in Hawaii, USA. This is the first report of an umbra-like virus found on figs in Crimea and outside of Hawaii, expanding information on the geographical distribution and genetic diversity of FULV. All of the Crimean FULV-positive plants were also co-infected with fig mosaic virus, fig badnavirus 1, and grapevine badna FI virus.

Features of the water regime and photosynthesis in hybrid forms of cherry plum under the dry wind season conditions

Background. The results of a study on the drought resistance of cherry plum hybrid forms are presented. Water retention capacity of leaves and chlorophyll fluorescence were measured under the simulated conditions close to the dry wind season.Materials and methods. The water regime parameters were studied for five cherry plum genotypes in 2021 and 2022. Leaves of four hybrid forms developed at the Nikita Botanical Gardens and the reference cherry plum hybrid cultivar ‘Rumyanaya Zorka’ (Prunus rossica Erem.) were taken into the experiments. Using the guidelines by G. N. Eremeev and A. I. Lishchuk, a series of experiments on controlled leaf wilt at the air temperature of +27°C and relative humidity of 30% were conducted on cherry plum to assess the functional state of the photosynthetic apparatus during the development of water stress under dry wind conditions. The experiments were carried out in a Binder climate chamber. Chlorophyll fluorescence was measured using a portable Floratest fluorometer. The measurements were based on the parameters of the chlorophyll fluorescence induction curve (CFI) obtained on native leaves. The leaves of cv. ‘Rumyanaya Zorka’ in the state of complete watering served as the reference.Results and discussion. Dependence was identified between chlorophyll fluorescence and moisture content in the leaves of the studied samples. The hybrids were found to respond to drought in different ways. A relatively increased ability to retain moisture during dehydration was observed in form 12/26 whose leaves gave off moisture more slowly and restored their turgor better. It is promising for cultivation in areas with insufficient water supply. Form 99/36 had the lowest potential drought resistance. Forms 99/14 and 9/28 occupied an intermediate position.

First Report and Complete Genome Characterization of Cherry Virus A and Little Cherry Virus 1 from Russia.

Virus diseases affect the yield and fruit quality and shorten the productive life of stone fruits (Prunus spp. in the family Rosaceae). Of over fifty known viruses infecting these crops, cherry virus A (CVA) is among the most common, and little cherry virus 1 (LChV1) is one of the most economically important. Using high-throughput sequencing, full-length genomes of CVA and LChV1 isolates, found on interspecies hybrids in the Prunus collection of the Nikita Botanical Gardens, Russia, were sequenced, assembled, and characterized. CVA was found in the P. cerasifera × P. armeniaca hybrid and in phylogenetic analysis clustered with non-cherry virus isolates. The LChV1 isolate Stepnoe was detected in ((P. cerasifera Ehrh. × P. armeniaca L.) × P. brigantiaca Vill.) trihybrid suggesting that both P. cerasifera and P. brigantiaca potentially can be the LChV1 hosts. The isolate Stepnoe was most closely related to the Greece isolate G15_3 from sweet cherry, sharing 77.3% identity at the nucleotide level. Possibly, the highly divergent Russian isolate represents one more phylogroup of this virus. This is the first report of CVA and LChV1 from Russia, expanding the information on their geographical distribution and genetic diversity.

Analysis of the Tomato Aspermy Virus Complete Genomes Suggests Reassortment in Russian Isolates from Chrysanthemum

Tomato aspermy virus (TAV, genus Cucumovirus from the family Bromoviridae) is one of the most common and harmful chrysanthemum viruses, causing severe flower distortion, size reduction and color breaking. Metatranscriptome sequencing of chrysanthemum plants of the Ribonette and Golden Standard cultivars from the collection of the Nikita Botanical Garden (Yalta, Republic of Crimea) generated TAV-related reads. The complete genomes of two Russian isolates of the virus were assembled from the reads obtained. This is the first report of full-length TAV genomes from Russia. Typically of cucumoviruses, the segmented TAV genome is represented by three single-stranded positive-sense linear RNA molecules with a length of 3412 (RNA1), 3097 (RNA2) and 2219 (RNA3) nucleotides. Five open reading frames (ORF) have been identified that encode replicase (ORF1), RNA-dependent RNA polymerase (ORF2a), silencing suppressor protein (OFR2b), movement protein (OFR3a) and the virus coat protein (ORF3b). The identity of the TAV genomes from the two chrysanthemum cultivars was 99.8% for all three viral RNAs, and with other TAV isolates from Genbank – 97.5–99.7 (RNA1), 93.8–99.8 (RNA2), and 89.3–99.3% (RNA3). Phylogenetic analysis showed that RNA1 and RNA3 of the Russian isolates were assigned to heterogeneous groups of TAV isolates found on various plant species in different regions of the world. At the same time, RNA2 clearly clustered with tomato isolates SKO20ST2 from Slovenia and PV-0220 from Bulgaria and, to a lesser extent, with the Iranian isolate Ker.Mah.P from petunia and the Chinese isolate Henan from chrysanthemum. The incongruence of phylogenetic trees reconstructed from different segments of the viral genome suggests pseudo-recombination (reassortment) in the Russian TAV isolates.

Whole Genome Characterization of Prunus Necrotic Ringspot Virus and Prune Dwarf Virus Infecting Stone Fruits in Russia

We conducted a survey of the phytosanitary status of the Prunus germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. The virome of plants displaying virus-like symptoms was studied using Illumina MiSeq high-throughput sequencing. Reads related to prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), and ourmia-like virus 1 (OuLV1) were generated in a number of samples. Near complete genomes of two divergent PNRSV isolates, PDV isolate, and a contig partly covered OuLV1 genome were assembled de novo using the metaSPAdes program. The structure of the genomic RNA1, RNA2, and RNA3 of the new ilarvirus isolates was shown to be typical of PNRSV and PDV. This is the first report and characterization of the PNRSV and PDV full-length genomes from Russia, expanding the information on their geographical distribution and genetic diversity. An open reading frames (ORF)-based phylogeny of all full-length PNRSV and PDV genomes available in GenBank divided each ORF into two or three main clusters. A number of isolates migrated from one cluster to another cluster, depending on the analyzed genome segment. The different branching order may indicate reassortment in the evolutionary history of some PDV and PNRSV isolates.

Study of the Component Composition of Essential Oil, Morphology, Anatomy and Ploidy Level of Hyssopus officinalis f. cyaneus Alef

Common hyssop (Hyssopus officinalis L.) is widely used as an aromatic and medicinal plant. In the component composition of the essential oil from the above-ground mass of H. officinalis f. cyaneus, from the collection of the Nikita Botanical Garden, the bicyclic monoterpene ketones isopinocamphone (50.99–64.41%) and pinocamphone (3.95–18.88%) predominate, which allows us to attribute this form to the isopinocamphone chemotype for use in pharmacology. An essential oil sample with a high content of isopinocamphone (70.74%) in complete absence of pinocamphone was determined, which made it possible to use the plant as a starting material for breeding. The objective of our work was to study the component composition of the essential oil of this form, and the morphology, anatomy and ploidy level of microshoots in vitro on a nutrient medium with BAP. This was compared with ex situ samples to develop a cultivation technique with the preservation of a valuable trait for use in task-oriented selection. Biotechnological methods are used for future mass propagation, study and the preservation of breeding forms. Morphological and anatomical features and ploidy of H. officinalis microshoots were studied in vitro. Using in vitro culturing of microshoots on MS medium containing BAP, a decrease in the cuticular layer and the degree of development of collenchyma near vascular bundles in leaves were shown compared to microshoots ex situ. Significant structural changes were found with a high increase in BAP concentration, while no changes in the ploidy level were detected.

Analysis of the Complete Tomato Aspermy Virus Genomes Suggests Reassortment in Russian Isolates from Chrysanthemum

Tomato aspermy virus (TAV, genus Cucumovirus from the family Bromoviridae) is one of the most common and harmful chrysanthemum viruses, causing severe flower distortion, size reduction, and color breaking. Metatranscriptome sequencing of chrysanthemum plants of the Ribonette and Golden Standard cultivars from the collection of the Nikita Botanical Garden (Yalta, Republic of Crimea) generated TAV-related RNA reads. The complete genomes of two Russian isolates of the virus were assembled from the reads. This is the first report of full-length TAV genomes from Russia. Typically of cucumoviruses, the segmented TAV genome is represented by three single-stranded positive-sense linear RNA molecules of 3412 (RNA1), 3097 (RNA2) and 2219 (RNA3) nucleotides. Five open reading frames (ORF) have been identified that encode replicase (ORF1), RNA-dependent RNA polymerase (ORF2a), silencing suppressor protein (OFR2b), movement protein (OFR3a) and the coat protein (ORF3b). The identity of TAV genomes from the two chrysanthemum cultivars was 99.8% for all three viral RNAs; with other TAV isolates from GenBank it was 97.5-99.7% (RNA1), 93.8-99.8% (RNA2), and 89.3-99.3% (RNA3). Phylogenetic analysis showed that RNA1 and RNA3 of the Russian isolates were assigned to heterogeneous groups of TAV isolates found on various plant species in different regions of the world. At the same time, RNA2 clearly clustered with tomato isolates SKO20ST2 from Slovenia and PV-0220 from Bulgaria and, to a lesser extent, with the Iranian isolate Ker.Mah.P from petunia and the Chinese isolate Henan from chrysanthemum. The incongruence of phylogenetic trees reconstructed from different genome segments suggests pseudo-recombination (reassortment) in the Russian TAV isolates.

Characterization of Divergent Grapevine Badnavirus 1 Isolates Found on Different Fig Species (Ficus spp.).

Fig mosaic disease is spread worldwide and is believed to have a viral etiology. Divergent isolates of grapevine badnavirus 1 (GBV1), named fGBV1, were discovered on Ficus carica, F. palmata, F. virgata, and F. afghanistanica in the fig germplasm collection of the Nikita Botanical Gardens, Russia, expanding the list of viruses infecting this crop. The complete genomes of five fGBV1 isolates from F. carica and F. palmata trees were determined using high-throughput and Sanger sequencing. The genomes comprised 7283 base pairs, contained four overlapping open reading frames, were 99.7 to 99.9% identical to each other, and related to GBV1 (83.2% identity). The reverse transcriptase RNase H genome regions of fGBV1 and GBV1 share 84.6% identity, indicating that fGBV1 is a divergent isolate of GBV1, which was found on the new natural hosts from a different family (Moraceae). Further, fGBV1-specific primers were developed to detect the virus using RT-PCR. Survey of 47 trees, belonging to four fig species and 14 local and introduced F. carica cultivars, showed the high fGBV1 prevalence in the collection (93.6%), including trees with no obvious symptoms of fig mosaic disease.

The age structure of the coepopulations of B<i>erberis</i><i>aquifolium</i> Purch in the Protected Areas of the Southern Coast of the Crimea

On the basis of generally accepted and modern methods and approaches, the age structure of the coenopopulations of Berberis aquifolium in semi-natural and natural communities in Protected Areas of the Southern Coast of the Crimea with different categories of protection ("Yalta Mountain Forest", "Cape Martyan", "Nikita Botanical Gardens") has been studied. It was found that the species in the surveyed territories occurs in different types of relatively closed (0.6-0.8) tree-shrub communities, at an altitude of 120 to 530 m above the sea level, on the slopes of different exposures, with a steepness from 5 to 45°. All the described coenopopulations are normal, incomplete, with a left-hand spectrum, in three of them the absolute maximum falls on young generative (g 1 - up to 38%), in two - on virginal (v - 25-53%), in one - on middle-aged generative (g 2 - 25%) plants. The ontogenetic structure of the studied coenopopulations is represented by two types: single-vertex and bimodal, according to the A.A. Uranov's, O.V. Smirnova's classification; by three types: maturing, transitional and mature, according to the "delta-omega" classification. Three coenopopulations belong to the group of unstable, with a weak degree of self-support, two ones - to promising, with a moderate degree of self-support, one - to promising, with effective self-support. The values of the recovery index (1.0-2.5) in promising coenopopulations indicate a sufficient potential of the species to maintain its structure by seed reproduction.

The assortment of small-flowered chrysanthemum promising for landscaping the Southern Coast of the Crimea and the Russian South

Numerous collections of flower plants are collected in the Nikitsky (Nikita) Botanical Gardens - National Scientific Center (NBG - NSC). Among them, a special place belongs to the garden chrysanthemum ( Chrysanthemum × morifolium (Ramat.) Hemsl.), since its quantitative and qualitative composition has no analogues in the territory of the Russian Federation. Currently, the collection includes 529 cultivars and forms of domestic and foreign breeding, of which 350 cultivars and forms belong to the small-flowered garden group. The article considers the studied and selected promising assortment of small-flowered chrysanthemum for landscaping the Southern Coast of the Crimea and the Russian South, which for successful implementation in urban landscaping is divided into groups according to the timing of flowering, the height of flowering shoots, color and types of inflorescences.

Highly divergent isolates of chrysanthemum virus B and chrysanthemum virus R infecting chrysanthemum in Russia.

BackgroundChrysanthemum is a popular ornamental and medicinal plant that suffers from many viruses and viroids. Among them, chrysanthemum virus B (CVB, genus Carlavirus, family Betaflexiviridae) is widespread in all chrysanthemum-growing regions. Another carlavirus, chrysanthemum virus R (CVR), has been recently discovered in China. Information about chrysanthemum viruses in Russia is very scarce. The objective of this work was to study the prevalence and genetic diversity of CVB and CVR in Russia.MethodsWe surveyed the chrysanthemum (Chrysanthemum morifolium Ramat.) germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. To detect CVB and CVR, we used RT-PCR with virus-specific primers. To reveal the complete genome sequences of CVB and CVR isolates, metatransciptomic analysis of the cultivars Ribonette, Fiji Yellow, and Golden Standard plants, naturally co-infected with CVB and CVR, was performed using Illumina high-throughput sequencing. The recombination detection tool (RDP4) was employed to search for recombination in assembled genomes.ResultsA total of 90 plants of 23 local and introduced chrysanthemum cultivars were surveyed. From these, 58 and 43% plants tested positive for CVB and CVR, respectively. RNA-Seq analysis confirmed the presence of CVB and CVR, and revealed tomato aspermy virus in each of the three transcriptomes. Six near complete genomes of CVB and CVR were assembled from the RNA-Seq reads. The CVR isolate X21 from the cultivar Golden Standard was 92% identical to the Chinese isolate BJ. In contrast, genomes of the CVR isolates X6 and X13 (from the cultivars Ribonette and Fiji Yellow, respectively), were only 76% to 77% identical to the X21 and BJ, and shared 95% identity to one another and appear to represent a divergent group of the CVR. Two distantly related CVB isolates, GS1 and GS2, were found in a plant of the cultivar Golden Standard. Their genomes shared from 82% to 87% identity to each other and the CVB genome from the cultivar Fiji Yellow (isolate FY), as well as to CVB isolates from Japan and China. A recombination event of 3,720 nucleotides long was predicted in the replicase gene of the FY genome. It was supported by seven algorithms implemented in RDP4 with statistically significant P-values. The inferred major parent was the Indian isolate Uttar Pradesh (AM765837), and minor parent was unknown.ConclusionWe found a wide distribution of CVB and CVR in the chrysanthemum germplasm collection of the Nikita Botanical Gardens, which is the largest in Russia. Six near complete genomes of CVR and CVB isolates from Russia were assembled and characterized for the first time. This is the first report of CVR in Russia and outside of China thus expanding the information on the geographical distribution of the virus. Highly divergent CVB and CVR isolates have been identified that contributes the better understanding the genetic diversity of these viruses.

ФОРМИРОВАНИЕ НОВОГО ТЕМАТИЧЕСКOГО САДА В НИКИТСКОМ БОТАНИЧЕСКОМ САДУ

The article presents the concept of theme garden within Nikita botanical gardens "The spring blooming garden" supposed to cover 0,97 ha and designed according to seasonal exposition law. In terms of the research the area general layout and visualization of certain segments of landscape gardening were worked out. There is also an area calculation, aimed for planting of ornamental cultures. The study cites the characteristics of the area, intended for spring blooming garden site, description of planning decision and organizing of the small garden structure, including the way of natural material usage for making small architectural forms. At the same time the research covers various compositions made of fruit-bearing, bulbous and other spring blooming plants, capable to grow under conditions of South coast of the Crimea due to their bioecological properties. Besides there are flowering terms and duration of plants introduced in the exposition, and a union calendar of the blooming period was composed as well.

Drought resistance of peach cultivars and forms of the Nikita Botanical Gardens collection

Drought resistance of peach cultivars and forms of the Nikita Botanical Gardens collection

Genetic Diversity of Peach Cultivars from the Collection of the Nikita Botanical Garden Based on SSR Markers.

The Nikita Botanical Garden (NBG) has a unique Prunus L. collection (peach, apricot, plum, cherry) comprising more than 3000 accessions. NBG is also a breeding center for stone fruits, including peach (Prunus persica (L.) Batsch). In the present study a set of 85 peach cultivars bred in NBG, Europe, and North America was analyzed using 12 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was comparable to the previous estimates of genetic variability in peach cultivars. The average number of alleles per locus was 5.67, PIC value averaged 0.49, expected, and observed heterozygosity averaged 0.52 and 0.31, respectively. Among the detected alleles, 19 (27.94%) were rare and 12 (17.65%) were unique. All studied accessions except two could be identified with the used marker set. Cluster analysis revealed some groups according to the cultivars’ pedigrees. No clear differentiation of the studied sample according to geographic origin or fruit characteristics of peach cultivars was revealed. The results provide valuable information for identification and rational management of the material preserved in the NBG peach collection.

Aromatic and medicinal plants diversity in the Nikita Botanical Gardens

Aromatic and medicinal plants diversity in the Nikita Botanical Gardens

The Nikita Botanical Gardens ornamental plants collections biodiversity extension

ISHS VIII International Scientific and Practical Conference on Biotechnology as an Instrument for Plant Biodiversity Conservation (Physiological, Biochemical, Embryological, Genetic and Legal Aspects) The Nikita Botanical Gardens ornamental plants collections biodiversity extension

Reproductive traits of some hybrid tea rose cultivars from the collection of the Nikita Botanical Gardens

ISHS VIII International Scientific and Practical Conference on Biotechnology as an Instrument for Plant Biodiversity Conservation (Physiological, Biochemical, Embryological, Genetic and Legal Aspects) Reproductive traits of some hybrid tea rose cultivars from the collection of the Nikita Botanical Gardens

Content of biologically active substances in fruits of hybrid peaches included in breeding pool of the Nikita Botanical Gardens

ISHS VIII International Scientific and Practical Conference on Biotechnology as an Instrument for Plant Biodiversity Conservation (Physiological, Biochemical, Embryological, Genetic and Legal Aspects) Content of biologically active substances in fruits of hybrid peaches included in breeding pool of the Nikita Botanical Gardens

Evaluation of the Nikita Botanical Garden’s genefund collection of persimmon with parameters of the model cultivar

ISHS VIII International Scientific and Practical Conference on Biotechnology as an Instrument for Plant Biodiversity Conservation (Physiological, Biochemical, Embryological, Genetic and Legal Aspects) Evaluation of the Nikita Botanical Garden's genefund collection of persimmon with parameters of the model cultivar

SSR-fingerprinting and genetic relationship study of modern peach cultivars from the germplasm collection of Nikita Botanical Gardens

ISHS VIII International Scientific and Practical Conference on Biotechnology as an Instrument for Plant Biodiversity Conservation (Physiological, Biochemical, Embryological, Genetic and Legal Aspects) SSR-fingerprinting and genetic relationship study of modern peach cultivars from the germplasm collection of Nikita Botanical Gardens