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Kiselev KV, Ogneva ZV, Dubrovina AS, Gabdola AZ, Khassanova GZ, Jatayev SA. Study of CaDreb2c and CaDreb2h Gene Sequences and Expression in Chickpea ( Cicer arietinum L.) Cultivars Growing in Northern Kazakhstan under Drought. PLANTS (BASEL, SWITZERLAND) 2024; 13:2066. [PMID: 39124184 PMCID: PMC11314285 DOI: 10.3390/plants13152066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Drought poses a significant challenge to plant growth and productivity, particularly in arid regions like northern Kazakhstan. Dehydration-responsive element-binding (DREB) transcription factors play an important role in plant response to drought and other abiotic stresses. In Arabidopsis thaliana, the DREB subfamily consists of six groups, designated DREB1 to DREB6. Among these, DREB2 is primarily associated with drought and salinity tolerance. In the chickpea genome, two DREB genes, CaDREB2c and CaDREB2h, have been identified, exhibiting high sequence similarity to Arabidopsis DREB2 genes. We investigated the nucleotide sequences of CaDREB2c and CaDREB2h genes in several chickpea cultivars commonly grown in northern Kazakhstan. Interestingly, the CaDREB2h gene sequence was identical across all varieties and corresponded to the sequence deposited in the GenBank. However, the CaDREB2c gene sequence exhibited variations among the studied varieties, categorized into three groups: the first group (I), comprising 20 cultivars, contained a CaDREB2c gene sequence identical to the GenBank (Indian cultivar CDC Frontier). The second group (II), consisting of 4 cultivars, had a single synonymous substitution (T to C) compared to the deposited CaDREB2c gene sequence. The third group, encompassing 5 cultivars, displayed one synonymous substitution (C to T) and two non-synonymous substitutions (G to T and G to A). Furthermore, we assessed the gene expression patterns of CaDREB2c and CaDREB2h in different chickpea varieties under drought conditions. Chickpea cultivars 8 (III), 37 (I), 6 (III), and 43 (I) exhibited the highest drought resistance. Our analysis revealed a strong positive correlation between drought resistance and CaDREB2h gene expression under drought stress. Our findings suggest that the chickpea's adaptive responses to water deprivation are associated with changes in CaDREB2 gene expression. To further elucidate the mechanisms underlying drought tolerance, we propose future research directions that will delve into the molecular interactions and downstream targets of CaDREB2 genes.
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Affiliation(s)
- Konstantin V. Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia; (Z.V.O.); (A.S.D.)
| | - Zlata V. Ogneva
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia; (Z.V.O.); (A.S.D.)
| | - Alexandra S. Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia; (Z.V.O.); (A.S.D.)
| | - Ademi Zh. Gabdola
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical Research University, Astana 010000, Kazakhstan; (A.Z.G.); (G.Z.K.); (S.A.J.)
| | - Gulmira Zh. Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical Research University, Astana 010000, Kazakhstan; (A.Z.G.); (G.Z.K.); (S.A.J.)
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy 021600, Kazakhstan
| | - Satyvaldy A. Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical Research University, Astana 010000, Kazakhstan; (A.Z.G.); (G.Z.K.); (S.A.J.)
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Aleynova OA, Nityagovsky NN, Ananev AA, Suprun AR, Ogneva ZV, Dneprovskaya AA, Beresh AA, Tyunin AP, Dubrovina AS, Kiselev KV. The Endophytic Microbiome of Wild Grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat Growing in the Russian Far East. PLANTS (BASEL, SWITZERLAND) 2023; 12:2952. [PMID: 37631163 PMCID: PMC10460016 DOI: 10.3390/plants12162952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023]
Abstract
Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61-65%) and Tremellomycetes (10-11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera's bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.
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Affiliation(s)
- Olga A. Aleynova
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Nikolay N. Nityagovsky
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Alexey A. Ananev
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Andrey R. Suprun
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Zlata V. Ogneva
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Alina A. Dneprovskaya
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
- The School of Natural Sciences, Far Eastern Federal University, 690090 Vladivostok, Russia
| | - Alina A. Beresh
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
- The School of Natural Sciences, Far Eastern Federal University, 690090 Vladivostok, Russia
| | - Alexey P. Tyunin
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Alexandra S. Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Konstantin V. Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East 27Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
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‘Unfinished’ Morphogenesis Hides Different Speciation Pathways in Charophytes: Evidence from the 190-Year-Old Original Material of Chara denudata (Charales, Charophyceae). DIVERSITY 2023. [DOI: 10.3390/d15020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Several Chara L. species have ‘unfinished’ morphogenesis that is recognizable because of their imperfect stem and branchlet cortication compared to the perfectly corticated species. Chara denudata A. Braun, described from South Africa, is one of these species, assumed for a long time to be conspecific with C. dissoluta A. Braun ex Leonhardi, as described from Central Europe. An attempt to resolve this long-lasting uncertainty in the framework of integrative taxonomy is implemented here. The restudy of the original material of both species showed similarities but did not identify a hiatus in their morphological traits, which represents evidence for their placement in the subsection Chara R.D. Wood according to morphology. Bifid adaxial bract cells, a trait rarely encountered among charophytes, were found for the first time in C. dissoluta. According to the rbcL and matK sequences, C. denudata was unexpectedly placed within the section Grovesia R.D. Wood, far from the clusters of the section Chara with C. dissoluta. This is in obvious disagreement with the position of C. denudata according to morphology. Both species were distinct according to their biology, habitat preference, and distribution and were accepted as distinct species. Therefore, the ‘unfinished’ morphogenesis resulting in morphological similarity hides different speciation pathways in charophytes.
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Aleynova OA, Nityagovsky NN, Suprun AR, Ananev AA, Dubrovina AS, Kiselev KV. The Diversity of Fungal Endophytes from Wild Grape Vitis amurensis Rupr. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212897. [PMID: 36365346 PMCID: PMC9654312 DOI: 10.3390/plants11212897] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 06/09/2023]
Abstract
Grapevine endophytic fungi have great potential for application in agriculture and represent an important source of various compounds with valuable biological activities. Wild grapevine is known to host a great number of rare and unidentified endophytes and may represent a rich repository of potential vineyard biocontrol agents. This investigation aimed to study the fungal endophytic community of wild grape Vitis amurensis Rupr. using a cultivation-dependent (fungi sowing) and a cultivation-independent (next-generation sequencing, NGS) approach. A comprehensive analysis of the endophytic fungal community in different organs of V. amurensis and under different environmental conditions has been performed. According to the NGS analysis, 12 taxa of class level were presented in different grapevine organs (stem, leaf, berry, seed). Among the 12 taxa, sequences of two fungal classes were the most represented: Dothideomycetes-60% and Tremellomycetes-33%. The top five taxa included Vishniacozyma, Aureobasidiaceae, Cladosporium, Septoria and Papiliotrema. The highest number of fungal isolates and sequences were detected in the grape leaves. The present data also revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic fungi in the wild Amur grape. The number of fungi recovered from grape tissues in autumn was two times higher than in summer. Thus, this study is the first to describe and analyze the biodiversity of the endophytic fungal community in wild grapevine V. amurensis.
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The Biodiversity of Grapevine Bacterial Endophytes of Vitis amurensis Rupr. PLANTS 2022; 11:plants11091128. [PMID: 35567129 PMCID: PMC9099740 DOI: 10.3390/plants11091128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
In this paper, the composition profiles of bacterial endophytes in wild-growing Amur grape Vitis amurensis Rupr. grown in the south of the Russian Far East were analyzed using both a cultivation-dependent (sowing bacteria) and a cultivation-independent (next generation sequencing, NGS) approach. Both methods revealed the prevalent endophytes in V. amurensis were represented by Gammaproteobacteria—40.3–75.8%, Alphaproteobacteria—8.6–18.7%, Actinobacteria—9.2–15.4%, and Bacilli—6.1–6.6%. NGS also showed a large proportion of Bacteroidia (12.2%) and a small proportion of other classes (less than 5.7%). In general, NGS revealed a greater variety of classes and genera in the endophytic bacterial community due to a high number of reads (574,207) in comparison with the number of colonies (933) obtained after the cultivation-dependent method. A comparative analysis performed in this study showed that both wild grape V. amurensis from Russia and domesticated cultivars of V. vinifera from Germany and California (USA) exhibit the same basic composition of endophytic bacteria, while the percentages of major taxa and minor taxa showed some differences depending on the plant organ, grape individuals, environmental conditions, and sampling time. Furthermore, the obtained data revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic bacteria in the wild Amur grape. Thus, this study firstly described and analyzed the biodiversity of endophytic bacteria in wild grapevine V. amurensis.
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Kiselev KV, Suprun AR, Aleynova OA, Ogneva ZV, Kostetsky EY, Dubrovina AS. The Specificity of Transgene Suppression in Plants by Exogenous dsRNA. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060715. [PMID: 35336598 PMCID: PMC8954795 DOI: 10.3390/plants11060715] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/16/2022] [Accepted: 03/06/2022] [Indexed: 05/03/2023]
Abstract
The phenomenon of RNA interference (RNAi) is widely used to develop new approaches for crop improvement and plant protection. Recent investigations show that it is possible to downregulate plant transgenes, as more prone sequences to silencing than endogenous genes, by exogenous application of double-stranded RNAs (dsRNAs) and small interfering RNAs (siRNAs). However, there are scarce data on the specificity of exogenous RNAs. In this study, we explored whether plant transgene suppression is sequence-specific to exogenous dsRNAs and whether similar effects can be caused by exogenous DNAs that are known to be perceived by plants and induce certain epigenetic and biochemical changes. We treated transgenic plants of Arabidopsis thaliana bearing the neomycin phosphotransferase II (NPTII) transgene with specific synthetic NPTII-dsRNAs and non-specific dsRNAs, encoding enhanced green fluorescent protein (EGFP), as well as with DNA molecules mimicking the applied RNAs. None of the EGFP-dsRNA doses resulted in a significant decrease in NPTII transgene expression in the NPTII-transgenic plants, while the specific NPTII-dsRNA significantly reduced NPTII expression in a dose-dependent manner. Long DNAs mimicking dsRNAs and short DNA oligonucleotides mimicking siRNAs did not exhibit a significant effect on NPTII transgene expression. Thus, exogenous NPTII-dsRNAs induced a sequence-specific and RNA-specific transgene-suppressing effect, supporting external application of dsRNAs as a promising strategy for plant gene regulation.
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Affiliation(s)
- Konstantin V. Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia; (K.V.K.); (A.R.S.); (O.A.A.); (Z.V.O.)
| | - Andrey R. Suprun
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia; (K.V.K.); (A.R.S.); (O.A.A.); (Z.V.O.)
| | - Olga A. Aleynova
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia; (K.V.K.); (A.R.S.); (O.A.A.); (Z.V.O.)
| | - Zlata V. Ogneva
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia; (K.V.K.); (A.R.S.); (O.A.A.); (Z.V.O.)
| | - Eduard Y. Kostetsky
- Department of Biochemistry, Microbiology and Biotechnology, Far Eastern Federal University, 690090 Vladivostok, Russia;
| | - Alexandra S. Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia; (K.V.K.); (A.R.S.); (O.A.A.); (Z.V.O.)
- Correspondence:
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Gontcharov AA, Nikulin AY, Nikulin VY, Bagmet VB, Allaguvatova RZ, Abdullin SR. New Species of Chloroidium (Trebouxiophyceae, Chlorophyta) from East Asia. PLANTS 2021; 10:plants10122560. [PMID: 34961032 PMCID: PMC8703672 DOI: 10.3390/plants10122560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022]
Abstract
Chlorella-like green algae that reproduce only asexually by immotile autospores or motile zoospores are the most typical inhabitants of non-aquatic environments. They have a simple morphology that hampers their differentiation, but algae of such habit represent a diverse array of lineages, which are mostly in the classes Chlorophyceae and Trebouxiophyceae. One of these lineages is the order Watanabeales (Watanabea clade; Trebouxiophyceae), which comprises 10 genera that share a distinct mode of reproduction through unequally sized autospores. Most of these genera account for a few species that are rarely recorded in nature. In contrast, the genus Chloroidium is one of the most species-rich and widely distributed members of the order. Three strains of coccoid green alga were isolated during a study of soil algae in the temperate monsoon climate zone of Asia. These strains are described here as a new species, Chloroidium orientalis. SSU and ITS rDNA sequence data, morphological characteristics, and life cycle features differentiate these strains from known members of the genus.
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Ravanrouy F, Niazi A, Moghadam A, Taghavi SM. MAP30 transgenic tobacco lines: from silencing to inducing. Mol Biol Rep 2021; 48:6719-6728. [PMID: 34420140 DOI: 10.1007/s11033-021-06662-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND DNA methylation is one of the most important epigenetic event that regulates gene expression. In addition to DNA methylation, transgene copy number may induce gene silencing. Therefore, the study of these cases is useful for understanding of gene silencing regulation. METHODS AND RESULTS In this study, the methylation pattern of 35S promoter was investigated in the second generation of MAP30 transgenic tobacco lines. Therefore, the genomic DNA melting curve changes were investigated before and after bisulfite treatment by real time PCR. To determine the exact position of methylation, the samples were sequenced after bisulfite treatment. Observation of decrease in DNA melting curve of expressing line in comparison with silenced line confirmed the presence of DNA methylation in silenced line. In order to induce the MAP30 expression, the silenced line was treated using different concentrations of Azacytidine and green tea extracts. The results showed that all concentrations of green tea extracts for 6 days and the concentrations of 3 and 10 μM Azacytidine for 10 and 3 days could induce the expression of MAP30 in silenced line respectively. Finally, the transgene copy number was estimated using real time PCR, as silenced line contained more than two copies while the lines expressing MAP30 contained only one or two copies. CONCLUSIONS Finally, we found that the presence of DNA methylation and also multiple gene copy numbers in silenced line have been led to gene silencing. Moreover, the effect of green tea extract on DNA methylation showed incredible results for the first time.
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Affiliation(s)
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran.
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran.
| | - Seyed Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
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Saber AA, Gontcharov AA, Nikulin AY, Nikulin VY, Rayan WA, Cantonati M. Integrative Taxonomic, Ecological and Genotyping Study of Charophyte Populations from the Egyptian Western-Desert Oases and Sinai Peninsula. PLANTS 2021; 10:plants10061157. [PMID: 34200166 PMCID: PMC8226818 DOI: 10.3390/plants10061157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
Present-day information available on the charophyte macroalgae in Egypt, including their phylogenetic affinities, remains largely incomplete. In this study, nine charophyte populations were collected from different aquatic biotopes across the Egyptian Western-Desert Oases and Sinai Peninsula. All populations were investigated using an integrative polyphasic approach including phylogenetic analyses inferred from the chloroplast-encoded gene (rbcL) and the internal transcribed spacer (ITS1) regions, in parallel with morphotaxonomic assignment, ultrastructure of the oospore walls, and autecology. The specimens identified belonged to the genera Chara, Nitella, and Tolypella, with predominance of the first genus to which five species were assigned though they presented some interesting aberrant taxonomic features: C. aspera, C. contraria, C. globata, C. tomentosa, and C. vulgaris. Based on our integrative study, the globally rare species C. globata was reported for the second time for the whole African continent. The genus Nitella was only represented by N. flagellifera, and based on the available literature, it is a new record for North Africa. Noteworthy, an interesting Tolypella sp., morphologically very similar to T. glomerata, was collected and characterized and finally designated with the working name 'Tolypella sp. PBA-1704 from a desert, freshwater wetland', mainly based on its concatenated rbcL+ITS1 phylogenetic position. This study not only improved our understanding on the diversity, biogeography and autecological preferences of charophytes in Egypt, but it also broadened our knowledge on this vulnerable algal group in North Africa, emphasizing the need of more in-depth research work in the future, particularly in the less-impacted desert habitats.
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Affiliation(s)
- Abdullah A. Saber
- Botany Department, Faculty of Science, Ain Shams University, Abbassia Square, Cairo 11566, Egypt; (A.A.S.); (W.A.R.)
| | - Andrey A. Gontcharov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159, 100-Letia Vladivostoka Prospect, 690022 Vladivostok, Russia; (A.A.G.); (A.Y.N.); (V.Y.N.)
| | - Arthur Yu. Nikulin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159, 100-Letia Vladivostoka Prospect, 690022 Vladivostok, Russia; (A.A.G.); (A.Y.N.); (V.Y.N.)
| | - Vyacheslav Yu. Nikulin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159, 100-Letia Vladivostoka Prospect, 690022 Vladivostok, Russia; (A.A.G.); (A.Y.N.); (V.Y.N.)
| | - Walaa A. Rayan
- Botany Department, Faculty of Science, Ain Shams University, Abbassia Square, Cairo 11566, Egypt; (A.A.S.); (W.A.R.)
| | - Marco Cantonati
- MUSE—Museo delle Scienze, Limnology & Phycology Section, Corso del Lavoro e della Scienza 3, I-38123 Trento, Italy
- Correspondence: ; Tel.: +39-0461-270342
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Bagmet VB, Abdullin SR, Mazina SE, Nikulin AY, Nikulin VY, Gontcharov AA. Life Cycle of Nitzschia palea (Kützing) W. Smith (Bacillariophyta). Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420020022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Muterko A, Salina E. VRN1-ratio test for polyploid wheat. PLANTA 2019; 250:1955-1965. [PMID: 31529399 DOI: 10.1007/s00425-019-03279-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/08/2019] [Indexed: 05/15/2023]
Abstract
The duplications of the dominantVrn-A1alleles as well as theVRN-B1gene, revealed for the first time, are new sources of polymorphism in polyploid wheat at these agronomically valuable genomic locations. Flowering time is an important trait in wheat breeding. In spring wheat, this feature is mainly determined by the variants and number of the homoeologous dominant VRN1 alleles. Previously, multiplication of the recessive vrn-A1 allele was shown for winter hexaploid wheat (Würschum et al., BMC Genet 29:16-96, 2015). In the present study, VRN1 gene copy-number variation as well as the copy number of VRN-A1 with the alternative exon 4 haplotype were investigated in spring and winter accessions of different tetraploid and hexaploid wheat species. Two ratio tests were optimized based on end-point quantification of PCR fragments and results were verified by a qPCR assay. It was defined that since the genomic environment affects the accessibility of amplified VRN1 regions, the DNA template should be fragmented for proper quantification of VRN1 copy number during PCR-based assays. For the first time, it was shown that the dominant Vrn-A1 alleles are most often duplicated in hexaploid wheat. In tetraploid wheat, both the dominant and recessive alleles were represented as a single haploid copy, and in only two accessions of T. dicoccum, vrn-A1b.3 was duplicated. Multiplication of VRN-A1 was often associated with awnless spikes. Five haploid combinations of the recessive vrn-A1 copies with alternative exon 4 were identified in hexaploid wheat. Finally for the first time, duplication of VRN-B1 was found in hexaploid wheat of T. compactum and T. spelta. These results expand our knowledge of the genetic diversity of VRN1 genes in wheat and provide additional strategies for the manipulation of flowering time in this strategic crop.
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Affiliation(s)
- Alexandr Muterko
- The Federal Research Center Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation.
| | - Elena Salina
- The Federal Research Center Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation
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Kiselev KV, Grigorchuk VP, Ogneva ZV, Suprun AR, Dubrovina AS. The effect of ultraviolet-C and precursor feeding on stilbene biosynthesis in spruce Picea jezoensis. JOURNAL OF PLANT PHYSIOLOGY 2019; 234-235:133-137. [PMID: 30784851 DOI: 10.1016/j.jplph.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
This study examines the effects of p-coumaric (CoA) and caffeic (CaA) acids on stilbene biosynthesis in one-year-old needles of Picea jezoensis (Lindl. et Gord.) Fisch ex Carr. under control conditions and after ultraviolet (UV-C) irradiation. HPLC analysis revealed that while UV-C irradiation slightly affected the total stilbene content, CoA and CaA feeding increased the total content of stilbenes by 1.2-1.3-fold. UV-C treatment combined with CoA-feeding of the P. jezoensis cuttings exerted the most pronounced stimulatory effect on stilbene accumulation leading to the total stilbene content of 9.18 mg/g of dry weight or DW. This increase correlated with the elevated transcription of the stilbene synthase PjSTS1a and PjSTS1b genes. UV-C treatment in combination with CaA feeding of P. jezoensis did not considerably influence stilbene content. These results revealed a positive effect of UV-C radiation and phenolic precursors on the content of stilbenes in spruce needles.
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Affiliation(s)
- K V Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia; Department of Biodiversity, The School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russia.
| | - V P Grigorchuk
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Z V Ogneva
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia; Department of Biodiversity, The School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russia
| | - A R Suprun
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia; Department of Biodiversity, The School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russia
| | - A S Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
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Kiselev KV, Aleynova OA, Grigorchuk VP, Dubrovina AS. Stilbene accumulation and expression of stilbene biosynthesis pathway genes in wild grapevine Vitis amurensis Rupr. PLANTA 2017; 245:151-159. [PMID: 27686467 DOI: 10.1007/s00425-016-2598-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
We detected and quantified six stilbenes ( cis -piceid, t -piceid, t -ε-viniferin, cis -ε-viniferin, t -resveratrol, and t -δ-viniferin) in the leaves, petioles, berry skins, and seeds of wild-growing Vitis amurensis . The highest content of stilbenes and expression of stilbene biosynthesis genes were in the probes collected in the autumn and after ultraviolet elicitation. Stilbenes, including the best-studied stilbene resveratrol, are known to display valuable bioactivities and protect plants against various pathogens. There is a lack of studies on stilbene quantities and spectrum combined with an analysis of the stilbene biosynthesis pathway gene expression in Vitaceae species, despite grapevine is an important source of stilbenes. This study presents an analysis of stilbene spectrum, stilbene content, and expression of stilbene biosynthesis genes both in natural conditions and after ultraviolet (UV-C) elicitation in the leaves, petioles, berry skins, and seeds of wild-growing Vitis amurensis, a highly stress-tolerant plant species. Using HPLC analysis, we detected six main stilbenes: cis-piceid (up to 0.257 mg/g of dry weight (DW) of plant material), t-piceid (up to 0.055 mg/g DW), t-ε-viniferin (up to 0.122 mg/g DW), cis-ε-viniferin (up to 0.031 mg/g DW), t-resveratrol (from 0.004 to 0.121 mg/g DW), and t-δ-viniferin (up to 0.019 mg/g DW). The stilbenes were actively synthesized in the leaves (total stilbenes 0.39 mg/g DW) and berry skins (total stilbenes 0.249 mg/g DW) of V. amurensis collected in the autumn. qRT-PCR revealed that the stilbene synthase (STS), resveratrol O-glucosyltransferase (Glu1), and polyphenol oxidase (PPO1) genes were actively expressed in the analyzed tissues. The resveratrol methyltransferase (Romt1) gene, which is known to catalyze biosynthesis of pterostilbene, was also expressed, but no pterostilbene has been detected in V. amurensis. The content of all detected stilbenes and expression of stilbene biosynthesis genes increased after UV-C treatment, except for Romt1. The data are important for understanding the stilbene biosynthesis in grapevine.
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Affiliation(s)
- Konstantin V Kiselev
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia, 690022.
- Department of Biotechnology and Microbiology, The School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russia, 690090.
| | - Olga A Aleynova
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia, 690022
| | - Valeria P Grigorchuk
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia, 690022
| | - Alexandra S Dubrovina
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia, 690022
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RolB gene-induced production of isoflavonoids in transformed Maackia amurensis cells. Appl Microbiol Biotechnol 2016; 100:7479-89. [DOI: 10.1007/s00253-016-7483-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 01/17/2023]
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15
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Baránek M, Čechová J, Raddová J, Holleinová V, Ondrušíková E, Pidra M. Dynamics and Reversibility of the DNA Methylation Landscape of Grapevine Plants (Vitis vinifera) Stressed by In Vitro Cultivation and Thermotherapy. PLoS One 2015; 10:e0126638. [PMID: 25973746 PMCID: PMC4431845 DOI: 10.1371/journal.pone.0126638] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/05/2015] [Indexed: 11/19/2022] Open
Abstract
There is relatively little information concerning long-term alterations in DNA methylation following exposure of plants to environmental stress. As little is known about the ratio of non-heritable changes in DNA methylation and mitotically-inherited methylation changes, dynamics and reversibility of the DNA methylation states were investigated in grapevine plants (Vitis vinifera) stressed by in vitro cultivation. It was observed that significant part of induced epigenetic changes could be repeatedly established by exposure to particular planting and stress conditions. However, once stress conditions were discontinued, many methylation changes gradually reverted and plants returned to epigenetic states similar to those of maternal plants. In fact, in the period of one to three years after in vitro cultivation it was difficult to distinguish the epigenetic states of somaclones and maternal plants. Forty percent of the observed epigenetic changes disappeared within a year subsequent to termination of stress conditions ending and these probably reflect changes caused by transient and reversible stress-responsive acclimation mechanisms. However, sixty percent of DNA methylation diversity remained after 1 year and probably represents mitotically-inherited epimutations. Sequencing of regions remaining variable between maternal and regenerant plants revealed that 29.3% of sequences corresponded to non-coding regions of grapevine genome. Eight sequences (19.5%) corresponded to previously identified genes and the remaining ones (51.2%) were annotated as "hypothetical proteins" based on their similarity to genes described in other species, including genes likely to undergo methylation changes following exposure to stress (V. vinifera gypsy-type retrotransposon Gret1, auxin-responsive transcription factor 6-like, SAM-dependent carboxyl methyltransferase).
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Affiliation(s)
- Miroslav Baránek
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Jana Čechová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Jana Raddová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Věra Holleinová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Eva Ondrušíková
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Miroslav Pidra
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
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