34 results on '"Brukhin V"'
Search Results
2. Basta tolerance as a selectable and screening marker for transgenic plants of Norway spruce
- Author
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Brukhin, V., Clapham, D., Elfstrand, M., and von Arnold, S.
- Published
- 2000
- Full Text
- View/download PDF
3. Proliferative activity of callus cultures of Taxus baccata L. in relation to anticancer diterpenoid taxol biosynthesis
- Author
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Brukhin, V. B., Moleva, I. R., Filonova, L. H., Grakhov, V. P., Blume, Ya. B., and Bozhkov, P. V.
- Published
- 1996
- Full Text
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4. SEssion 06 Morphogenesisin vitro
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Albrechtová, J. T. P., Cvikrová, M., Eder, J., Arente, G., Ievinsh, G., Gerinere, D., Borkovec, V., Klemš, M., Havel, L., Procházka, S., Brukhin, V. B., Batygina, T. B., Buddendorf-Joosten, J. M. C., Woltering, E. J., Burdová, I., Opatrná, J., Emons, A. M. C., Gartland, J. S., Fenning, T. M., Brasier, C. M., Gartland, K. M. A., Griga, M., Stejskal, J., Grospietsch, M., Lipavská, H., Harvey, B. M. R., Staikidou, I., Fraser, T. W., Selby, C., Heloir, M. C., Kevers, C., Hausman, J. F., Gaspar, Th., Hollo, R., Misik, S., Hrubcová, M., Čeřovská, N., Isaeva, N. A., Jasik, J., Lenard, M., Chauvin, J. E., Cohat, J., Kákoniová, D., Lišková, D., Auxtová, O., KubaČková, M., Karácsonyi, Š., Bilisics, L., Kaya, Z., Gokce, F., Kromer, K. D., Lux, A., Ordóńez, J. Ruiz, López, A. Pińeyro, Mensuali-Sodi, A., Panizza, M., Tognoni, F., Mirković, K., Economou, A. S., Lionakis, S. T., Molnár, Z., Noe, N., Papathanasiou, F., Pavlova, M. K., Podlutsky, A. G., Sokolova, O. A., Radojevic, Lj., Marinkovic, N., Salmenkallio-Marttila, M., Kauppinen, V., šamaj, J., Bobák, M., Blehová, A., Krištín, J., Siminis, C. I., Kanellis, A. K., Roubelakis-Angelakis, K. A., Sińska, I., Zarska-Maciejewska, B., Sladký, Z., Stiborová, I., Berná, K., Tichá, I., Torne, J. M., Rodriguez, P., Camara, T., Claparols, I., Santos, M., Verbaere, C., Vlašínová, H., Zenkteler, E., and Urbaniak, L.
- Published
- 1994
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5. Molecular and genetic regulation of apomixis
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Brukhin, V., primary
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- 2017
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6. Plastids and mitochondria comportment in dividing meiocytes of Psilotum nudum
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Tchórzewska, D., primary, Brukhin, V. B., additional, and Bednara, J., additional
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- 2014
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7. Plant Growth and Development - Basic Knowledge and Current Views
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Brukhin, V., primary and Morozova, N., additional
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- 2010
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8. Plant Growth and Development - Basic Knowledge and Current Views.
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Brukhin, V. and Morozova, N.
- Subjects
- *
PLANT development , *BIOLOGICAL mathematical modeling , *MORPHOGENESIS , *PLANT morphology , *PLANT genetics , *PLANT cell cycle - Abstract
One of the most intriguing questions in life science is how living organisms develop and maintain their predominant form and shape via the cascade of the processes of differentiation starting from the single cell. Mathematical modeling of these developmental processes could be a very important tool to properly describe the complex processes of evolution and geometry of morphogenesis in time and space. Here, we summarize the most important biological knowledge on plant development, exploring the different layers of investigation in developmental processes such as plant morphology, genetics, plant physiology, molecular biology and epigenetics. As knowledge on the fundamentals of plant embryogenesis, growth and development is constantly improving, we gather here the latest data on genetic, molecular and hormonal regulation of plant development together with the basic background knowledge. Special emphasis is placed on the regulation of cell cycle progression, on the role of the signal molecules phytohormones in plant development and on the details of plant meristems (loci containing plant stem cells) function. We also explore several proposed biological models regarding regulating plant development. The information presented here could be used as a basis for mathematical modeling and computer simulation of developmental processes in plants. [ABSTRACT FROM PUBLISHER]
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- 2011
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9. Two waves of programmed cell death occur during formation and development of somatic embryos in the gymnosperm, Norway spruce.
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H, Filonova L, V, Bozhkov P, B, Brukhin V, G, Daniel, B, Zhivotovsky, and S, von Arnold
- Abstract
In the animal life cycle, the earliest manifestations of programmed cell death (PCD) can already be seen during embryogenesis. The aim of this work was to determine if PCD is also involved in the elimination of certain cells during plant embryogenesis. We used a model system of Norway spruce somatic embryogenesis, which represents a multistep developmental pathway with two broad phases. The first phase is represented by proliferating proembryogenic masses (PEMs). The second phase encompasses development of somatic embryos, which arise from PEMs and proceed through the same sequence of stages as described for their zygotic counterparts. Here we demonstrate two successive waves of PCD, which are implicated in the transition from PEMs to somatic embryos and in correct embryonic pattern formation, respectively. The first wave of PCD is responsible for the degradation of PEMs when they give rise to somatic embryos. We show that PCD in PEM cells and embryo formation are closely interlinked processes, both stimulated upon withdrawal or partial depletion of auxins and cytokinins. The second wave of PCD eliminates terminally differentiated embryo-suspensor cells during early embryogeny. During the dismantling phase of PCD, PEM and embryo-suspensor cells exhibit progressive autolysis, resulting in the formation of a large central vacuole. Autolytic degradation of the cytoplasm is accompanied by lobing and budding-like segmentation of the nucleus. Nuclear DNA undergoes fragmentation into both large fragments of about 50 kb and multiples of approximately 180 bp. The tonoplast rupture is delayed until lysis of the cytoplasm and organelles, including the nucleus, is almost complete. The protoplasm then disappears, leaving a cellular corpse represented by only the cell wall. This pathway of cell dismantling suggests overlapping of apoptotic and autophagic types of PCD during somatic embryogenesis in Norway spruce.
- Published
- 2000
10. SEssion 06 Morphogenesis in vitro
- Author
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Albrechtová, J., Cvikrová, M., Eder, J., Arente, G., Ievinsh, G., Gerinere, D., Borkovec, V., Klemš, M., Havel, L., Procházka, S., Brukhin, V., Batygina, T., Buddendorf-Joosten, J., Woltering, E., Burdová, I., Opatrná, J., Emons, A., Gartland, J., Fenning, T., Brasier, C., Gartland, K., Griga, M., Stejskal, J., Grospietsch, M., Lipavská, H., Harvey, B., Staikidou, I., Fraser, T., Selby, C., Heloir, M., Kevers, C., Hausman, J., Gaspar, Th., Hollo, R., Misik, S., Hrubcová, M., Čeřovská, N., Isaeva, N., Jasik, J., Lenard, M., Chauvin, J., Cohat, J., Kákoniová, D., Lišková, D., Auxtová, O., KubaČková, M., Karácsonyi, Š., Bilisics, L., Kaya, Z., Gokce, F., Kromer, K., Lux, A., Ordóńez, J., López, A., Mensuali-Sodi, A., Panizza, M., Tognoni, F., Mirković, K., Economou, A., Lionakis, S., Molnár, Z., Noe, N., Papathanasiou, F., Pavlova, M., Podlutsky, A., Sokolova, O., Radojevic, Lj., Marinkovic, N., Salmenkallio-Marttila, M., Kauppinen, V., šamaj, J., Bobák, M., Blehová, A., Krištín, J., Siminis, C., Kanellis, A., Roubelakis-Angelakis, K., Sińska, I., Zarska-Maciejewska, B., Sladký, Z., Stiborová, I., Berná, K., Tichá, I., Torne, J., Rodriguez, P., Camara, T., Claparols, I., Santos, M., Verbaere, C., Vlašínová, H., Zenkteler, E., and Urbaniak, L.
- Published
- 1994
- Full Text
- View/download PDF
11. Proliferative activity of callus cultures of Taxus baccataL. in relation to anticancer diterpenoid taxol biosynthesis
- Author
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Brukhin, V., Moleva, I., Filonova, L., Grakhov, V., Blume, Ya., and Bozhkov, P.
- Abstract
Stable growing callus cultures were recovered from stem segments of Taxus baccata. Callus developed from the peridermal cells. The content of taxol in callus tissues varied in the range of [0.0003–0.001% on dry weight basis] and was higher in fast growing calli compared to slow growing calli.
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- 1996
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12. Flower development schedule in tomato Lycopersicon esculentum cv. sweet cherry
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Brukhin, V., Michel Hernould, Nathalie Gonzalez, Chevalier, C., Armand Mouras, Station de physiologie végétale, Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,HISTOLOGIE ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
13. Putting Russia on the genome map
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Oleksyk Taras, Brukhin, V., O Brien, S. J., and Sills, J.
14. The angiosperm female gametophyte: No longer the forgotten generation
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Brukhin, V., Curtis, M. D., and Ueli Grossniklaus
15. Two waves of programmed cell death occur during formation and development of somatic embryos in the gymnosperm, Norway spruce
- Author
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Filonova, L. H., Bozhkov, P. V., Brukhin, V. B., Geoffrey Daniel, Zhivotovsky, B., and Arnold, S.
16. Plastids and mitochondria comportment in dividing meiocytes of Psilotum nudum
- Author
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Tchórzewska, D., Brukhin, V. B., Bednara, J., Tchórzewska, D., Brukhin, V. B., and Bednara, J.
- Abstract
In prophase I meiocyte plastids and mitochondria were situated at random. By telophase I plastids and mitochondria were aggregated in an equatorial plane. The aggregation was differentiated into three layers, the middle layer formed mostly by mitochondria, the outer layers consisted largely of plastids. By telophase II the mitochondria layers separated the cell into four domains, while plastid layers were disaggregated. Inside the mitochondrial layer the cell plates were formed. During this process mitochondria layers gradualy disintegrated. During prophase I to telophase I numerous plastids seem to undergo divisions. The telophase I layer mitochondria seemed to give rise to small electron-lucent vesicles.
17. First Genome of Rock Lizard Darevskia valentini Involved in Formation of Several Parthenogenetic Species.
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Ochkalova S, Korchagin V, Vergun A, Urin A, Zilov D, Ryakhovsky S, Girnyk A, Martirosyan I, Zhernakova DV, Arakelyan M, Danielyan F, Kliver S, Brukhin V, Komissarov A, and Ryskov A
- Subjects
- Animals, Genome genetics, Microsatellite Repeats, Parthenogenesis genetics, Phylogeny, Lizards genetics
- Abstract
The extant reptiles are one of the most diverse clades among terrestrial vertebrates and one of a few groups with instances of parthenogenesis. Due to the hybrid origin of parthenogenetic species, reference genomes of the parental species as well as of the parthenogenetic progeny are indispensable to explore the genetic foundations of parthenogenetic reproduction. Here, we report on the first genome assembly of rock lizard Darevskia valentini , a paternal species for several parthenogenetic lineages. The novel genome was used in the reconstruction of the comprehensive phylogeny of Squamata inferred independently from 7369 trees of single-copy orthologs and a supermatrix of 378 conserved proteins. We also investigated Hox clusters, the loci that are often regarded as playing an important role in the speciation of animal groups with drastically diverse morphology. We demonstrated that Hox clusters of D. valentini are invaded with transposons and contain the HoxC1 gene that has been considered to be lost in the amniote ancestor. This study provides confirmation for previous works and releases new genomic data that will contribute to future discoveries on the mechanisms of parthenogenesis as well as support comparative studies among reptiles.
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- 2022
- Full Text
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18. Phylogenetic and Expression Analysis of CENH3 and APOLLO Genes in Sexual and Apomictic Boechera Species.
- Author
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Bakin E, Sezer F, Özbilen A, Kilic I, Uner B, Rayko M, Taskin KM, and Brukhin V
- Abstract
Apomictic plants (reproducing via asexual seeds), unlike sexual individuals, avoid meiosis and egg cell fertilization. Consequently, apomixis is very important for fixing maternal genotypes in the next plant generations. Despite the progress in the study of apomixis, molecular and genetic regulation of the latter remains poorly understood. So far APOLLO gene encoding aspartate glutamate aspartate aspartate histidine exonuclease is one of the very few described genes associated with apomixis in Boechera species. The centromere-specific histone H3 variant encoded by CENH3 gene is essential for cell division. Mutations in CENH3 disrupt chromosome segregation during mitosis and meiosis since the attachment of spindle microtubules to a mutated form of the CENH3 histone fails. This paper presents in silico characteristic of APOLLO and CENH3 genes, which may affect apomixis. Furthermore, we characterize the structure of CENH3 by bioinformatic tools, study expression levels of APOLLO and CENH3 transcripts by Real-Time Polymerase Chain Reaction RT-PCR in gynoecium/siliques of the natural diploid apomictic and sexual Boechera species at the stages of meiosis and before and after fertilization. While CENH3 was a single copy gene in all Boechera species, the APOLLO gene have several polymorphic alleles associated with sexual and apomictic reproduction in the Boechera genera. Expression of the APOLLO apo-allele during meiosis was upregulated in gynoecium of apomict B. divaricarpa downregulating after meiosis until the 4th day after pollination (DAP). On the 5th DAP, expression in apomictic siliques increased again. In sexual B. stricta gynoecium and siliques APOLLO apo-allele did not express. Expression of the APOLLO sex-allele during and after meiosis in gynoecium of sexual plants was several times higher than that in apomictic gynoecium. However, after pollination the sex-allele was downregulated in sexual siliques to the level of apomicts and increased sharply on the 5th DAP, while in apomictic siliques it almost did not express. At the meiotic stage, the expression level of CENH3 in the gynoecium of apomicts was two times lower than that of the sexual Boechera , decreasing in both species after meiosis and keep remaining very low in siliques of both species for several days after artificial pollination until the 4th DAP, when the expression level raised in sexual B. stricta siliques exceeding 5 times the level in apomictic B. divaricarpa siliques. We also discuss polymorphism and phylogeny of the APOLLO and CENH3 genes. The results obtained may indicate to a role of the CENH3 and APOLLO genes in the development of apomixis in species of the genus Boechera .
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- 2022
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19. Epigenetic Modifications in Plant Development and Reproduction.
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Brukhin V and Albertini E
- Abstract
Plants are exposed to highly fluctuating effects of light, temperature, weather conditions, and many other environmental factors throughout their life. As sessile organisms, unlike animals, they are unable to escape, hide, or even change their position. Therefore, the growth and development of plants are largely determined by interaction with the external environment. The success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addition to how environmental factors can change the patterns of genes expression, epigenetic regulation determines how genetic expression changes during the differentiation of one cell type into another and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many 'epigenomes'. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction when epigenetic marks are eliminated during meiosis and early embryogenesis and later reappear. However, during asexual plant reproduction, when meiosis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adaptive significance. In asexuals, epigenetic regulation is of particular importance for imparting plasticity to the phenotype when, apart from mutations, the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review.
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- 2021
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20. Epigenetic Control in Plants.
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Brukhin V
- Abstract
Epigenetic regulation in plants is an exciting field of research [...].
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- 2020
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21. Genome-wide sequence analyses of ethnic populations across Russia.
- Author
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Zhernakova DV, Brukhin V, Malov S, Oleksyk TK, Koepfli KP, Zhuk A, Dobrynin P, Kliver S, Cherkasov N, Tamazian G, Rotkevich M, Krasheninnikova K, Evsyukov I, Sidorov S, Gorbunova A, Chernyaeva E, Shevchenko A, Kolchanova S, Komissarov A, Simonov S, Antonik A, Logachev A, Polev DE, Pavlova OA, Glotov AS, Ulantsev V, Noskova E, Davydova TK, Sivtseva TM, Limborska S, Balanovsky O, Osakovsky V, Novozhilov A, Puzyrev V, and O'Brien SJ
- Subjects
- Adult, Communicable Diseases genetics, Demography, Haplotypes, Humans, INDEL Mutation, Pharmacogenetics, Phenotype, Phylogeography, Polymorphism, Single Nucleotide, Russia ethnology, Selection, Genetic, Whole Genome Sequencing, Genetic Variation
- Abstract
The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show allele frequency divergence from neighboring populations. Population genetics analyses revealed six phylogeographic partitions among indigenous ethnicities corresponding to their geographic locales. This study presents a characterization of population-specific genomic variation in Russia with results important for medical genetics and for understanding the dynamic population history of the world's largest country., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2020
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22. A brief note on genes that trigger components of apomixis.
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Brukhin V and Baskar R
- Subjects
- Biological Evolution, Gene Ontology, Molecular Sequence Annotation, Phylogeny, Plants classification, Apomixis genetics, Gene Expression Regulation, Plant, Genes, Plant, Plants genetics, Seeds genetics
- Abstract
Apomixis or asexual reproduction through seeds occurs in about 400 species of flowering plants producing genetically uniform progeny. During apomixis, meiosis is bypassed and embryos develop by parthenogenesis. However, the endosperm could form either autonomously without fertilization or sexually, depending on the plant species. Most probably, a heterochronic expression of sexually expressed genes is one of the reason that causes apomixis. A better understanding of the genetic components regulating apomixis is important for developmental and evolutionary studies and also for engineering apomixis traits into crop plants that may realize a possibility to propagate hybrid vigor in a range of subsequent generations.
- Published
- 2019
23. The Boechera Genus as a Resource for Apomixis Research.
- Author
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Brukhin V, Osadtchiy JV, Florez-Rueda AM, Smetanin D, Bakin E, Nobre MS, and Grossniklaus U
- Abstract
The genera Boechera (A. Löve et D. Löve) and Arabidopsis , the latter containing the model plant Arabidopsis thaliana , belong to the same clade within the Brassicaceae family. Boechera is the only among the more than 370 genera in the Brassicaceae where apomixis is well documented. Apomixis refers to the asexual reproduction through seed, and a better understanding of the underlying mechanisms has great potential for applications in agriculture. The Boechera genus currently includes 110 species (of which 38 are reported to be triploid and thus apomictic), which are distributed mostly in the North America. The apomictic lineages of Boechera occur at both the diploid and triploid level and show signs of a hybridogenic origin, resulting in a modification of their chromosome structure, as reflected by alloploidy, aneuploidy, substitutions of homeologous chromosomes, and the presence of aberrant chromosomes. In this review, we discuss the advantages of the Boechera genus to study apomixis, consider its modes of reproduction as well as the inheritance and possible mechanisms controlling apomixis. We also consider population genetic aspects and a possible role of hybridization at the origin of apomixis in Boechera. The molecular tools available to study Boechera , such as transformation techniques, laser capture microdissection, analysis of transcriptomes etc. are also discussed. We survey available genome assemblies of Boechera spp. and point out the challenges to assemble the highly heterozygous genomes of apomictic species. Due to these challenges, we argue for the application of an alternative reference-free method for the comparative analysis of such genomes, provide an overview of genomic sequencing data in the genus Boechera suitable for such analysis, and provide examples of its application.
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- 2019
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24. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.
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Kliver S, Rayko M, Komissarov A, Bakin E, Zhernakova D, Prasad K, Rushworth C, Baskar R, Smetanin D, Schmutz J, Rokhsar DS, Mitchell-Olds T, Grossniklaus U, and Brukhin V
- Abstract
Closely related to the model plant Arabidopsis thaliana , the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera , and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species ., Competing Interests: The authors declare no conflict of interest.
- Published
- 2018
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25. Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds.
- Author
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Yurchenko A, Yudin N, Aitnazarov R, Plyusnina A, Brukhin V, Soloshenko V, Lhasaranov B, Popov R, Paronyan IA, Plemyashov KV, and Larkin DM
- Subjects
- Animals, Genotyping Techniques, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Russia, Breeding, Cattle genetics, Genetic Profile, Genetics, Population
- Abstract
One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.
- Published
- 2018
- Full Text
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26. Genomic legacy of the African cheetah, Acinonyx jubatus.
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Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Küntzel A, Koepfli KP, Johnson W, Kuderna LF, García-Pérez R, Manuel Md, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, and O'Brien SJ
- Subjects
- Animals, Cats, Dogs, Genetic Variation, Genomics, Male, Multigene Family, Acinonyx genetics, Genome
- Abstract
Background: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations., Results: Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084-12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah's extremely high (>80 %) pleiomorphic sperm., Conclusions: The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species' natural history, physiological adaptations and unique reproductive disposition.
- Published
- 2015
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27. Putting Russia on the genome map.
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Oleksyk TK, Brukhin V, and O'Brien SJ
- Subjects
- Humans, DNA genetics, DNA Mutational Analysis, Genome, Human genetics
- Published
- 2015
- Full Text
- View/download PDF
28. The Genome Russia project: closing the largest remaining omission on the world Genome map.
- Author
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Oleksyk TK, Brukhin V, and O'Brien SJ
- Subjects
- Humans, Russia, Genome, Human
- Abstract
We are witnessing the great era of genome exploration of the world, as genetic variation in people is being detailed across multiple varied world populations in an effort unprecedented since the first human genome sequence appeared in 2001. However, these efforts have yet to produce a comprehensive mapping of humankind, because important regions of modern human civilization remain unexplored. The Genome Russia Project promises to fill one of the largest gaps, the expansive regions across the Russian Federation, informing not just medical genomics of the territories, but also the migration settlements of historic and pre-historic Eurasian peoples.
- Published
- 2015
- Full Text
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29. Annotated features of domestic cat - Felis catus genome.
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Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, Marques-Bonet T, Menotti-Raymond M, David VA, Narfström K, and O'Brien SJ
- Abstract
Background: Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors., Findings: Here we report a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia (MO, USA), bisulfite sequencing of Boris, a male cat from St. Petersburg (Russia), and light 30× sequencing of Sylvester, a European wildcat progenitor of cat domestication. The annotation includes 21,865 protein-coding genes identified by a comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements, and 3,182 microRNA homologues. The methylation sites study shows that 10.5% of cat genome cytosines are methylated. An assisted assembly of a European wildcat, Felis silvestris silvestris, was performed; variants between F. silvestris and F. catus genomes were derived and compared to F. catus., Conclusions: The presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing. The assembly and its annotation offer an important resource for connecting the rich veterinary and natural history of cats to genome discovery.
- Published
- 2014
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30. The Arabidopsis CUL4-DDB1 complex interacts with MSI1 and is required to maintain MEDEA parental imprinting.
- Author
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Dumbliauskas E, Lechner E, Jaciubek M, Berr A, Pazhouhandeh M, Alioua M, Cognat V, Brukhin V, Koncz C, Grossniklaus U, Molinier J, and Genschik P
- Subjects
- Amino Acid Sequence, Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins physiology, Cullin Proteins genetics, Cullin Proteins physiology, DNA-Binding Proteins genetics, DNA-Binding Proteins physiology, Gene Expression Regulation, Plant, Genomic Imprinting genetics, Molecular Sequence Data, Multiprotein Complexes metabolism, Multiprotein Complexes physiology, Plants, Genetically Modified, Protein Binding physiology, Repressor Proteins genetics, Repressor Proteins metabolism, Repressor Proteins physiology, Sequence Homology, Amino Acid, Ubiquitination physiology, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Cullin Proteins metabolism, DNA-Binding Proteins metabolism, Genomic Imprinting physiology
- Abstract
Protein ubiquitylation regulates a broad variety of biological processes in all eukaryotes. Recent work identified a novel class of cullin-containing ubiquitin ligases (E3s) composed of CUL4, DDB1, and one WD40 protein, believed to act as a substrate receptor. Strikingly, CUL4-based E3 ligases (CRL4s) have important functions at the chromatin level, including responses to DNA damage in metazoans and plants and, in fission yeast, in heterochromatin silencing. Among putative CRL4 receptors we identified MULTICOPY SUPPRESSOR OF IRA1 (MSI1), which belongs to an evolutionary conserved protein family. MSI1-like proteins contribute to different protein complexes, including the epigenetic regulatory Polycomb repressive complex 2 (PRC2). Here, we provide evidence that Arabidopsis MSI1 physically interacts with DDB1A and is part of a multimeric protein complex including CUL4. CUL4 and DDB1 loss-of-function lead to embryo lethality. Interestingly, as in fis class mutants, cul4 mutants exhibit autonomous endosperm initiation and loss of parental imprinting of MEDEA, a target gene of the Arabidopsis PRC2 complex. In addition, after pollination both MEDEA transcript and protein accumulate in a cul4 mutant background. Overall, our work provides the first evidence of a physical and functional link between a CRL4 E3 ligase and a PRC2 complex, thus indicating a novel role of ubiquitylation in the repression of gene expression.
- Published
- 2011
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31. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome.
- Author
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Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, and Belostotsky DA
- Subjects
- Arabidopsis genetics, Arabidopsis Proteins genetics, Exoribonucleases genetics, Exosome Multienzyme Ribonuclease Complex, Gene Expression Regulation, Plant, Genotype, MicroRNAs metabolism, Molecular Sequence Data, Mutation, Nuclear Proteins metabolism, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis, Peptide Mapping, Phenotype, RNA chemistry, RNA Interference, RNA, Messenger metabolism, RNA, Small Interfering metabolism, RNA, Untranslated metabolism, Tandem Mass Spectrometry, Arabidopsis metabolism, Arabidopsis Proteins metabolism, Chromosome Mapping methods, Exoribonucleases metabolism, Gene Expression Profiling methods, Plants, Genetically Modified metabolism, Proteomics methods, RNA metabolism
- Abstract
The exosome complex plays a central and essential role in RNA metabolism. However, comprehensive studies of exosome substrates and functional analyses of its subunits are lacking. Here, we demonstrate that as opposed to yeast and metazoans the plant exosome core possesses an unanticipated functional plasticity and present a genome-wide atlas of Arabidopsis exosome targets. Additionally, our study provides evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants, reveals unexpected aspects of stable structural RNA metabolism, and uncovers numerous novel exosome substrates. These include a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described and belong to a layer of the transcriptome that can only be visualized upon inhibition of exosome activity. These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes.
- Published
- 2007
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32. The RPN1 subunit of the 26S proteasome in Arabidopsis is essential for embryogenesis.
- Author
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Brukhin V, Gheyselinck J, Gagliardini V, Genschik P, and Grossniklaus U
- Subjects
- Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Cell Division genetics, Cyclin B genetics, Cyclin B metabolism, Cyclin B1, Embryonic Development genetics, Gametogenesis genetics, Gene Expression Regulation, Plant genetics, Genes, Lethal genetics, Mutation genetics, Phenotype, Proteasome Endopeptidase Complex genetics, Protein Isoforms genetics, Protein Isoforms metabolism, Protein Subunits genetics, Protein Subunits metabolism, Saccharomyces cerevisiae Proteins genetics, Saccharomyces cerevisiae Proteins metabolism, Seeds genetics, Arabidopsis embryology, Arabidopsis Proteins metabolism, Proteasome Endopeptidase Complex metabolism, Seeds metabolism
- Abstract
The 26S proteasome plays a central role in the degradation of regulatory proteins involved in a variety of developmental processes. It consists of two multisubunit protein complexes: the proteolytic core protease and the regulatory particle (RP). The function of most RP subunits is poorly understood. Here, we describe mutants in the Arabidopsis thaliana RPN1 subunit, which is encoded by two paralogous genes, RPN1a and RPN1b. Disruption of RPN1a caused embryo lethality, while RPN1b mutants showed no obvious abnormal phenotype. Embryos homozygous for rpn1a arrested at the globular stage with defects in the formation of the embryonic root, the protoderm, and procambium. Cyclin B1 protein was not degraded in these embryos, consistent with cell division defects. Double mutant plants (rpn1a/RPN1a rpn1b/rpn1b) produced embryos with a phenotype indistinguishable from that of the rpn1a single mutant. Thus, despite their largely overlapping expression patterns in flowers and developing seeds, the two isoforms do not share redundant functions during gametogenesis and embryogenesis. However, complementation of the rpn1a mutation with the coding region of RPN1b expressed under the control of the RPN1a promoter indicates that the two RPN1 isoforms are functionally equivalent. Overall, our data indicate that RPN1 activity is essential during embryogenesis, where it might participate in the destruction of a specific set of protein substrates.
- Published
- 2005
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33. Arabidopsis CUL3A and CUL3B genes are essential for normal embryogenesis.
- Author
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Thomann A, Brukhin V, Dieterle M, Gheyeselinck J, Vantard M, Grossniklaus U, and Genschik P
- Subjects
- Amino Acid Sequence, Arabidopsis embryology, Arabidopsis Proteins, Cell Cycle, Cullin Proteins, DNA, Bacterial genetics, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Germination, Molecular Sequence Data, Mutation, Phenotype, Promoter Regions, Genetic genetics, Seeds genetics, Seeds growth & development, Sequence Homology, Amino Acid, Arabidopsis genetics, Carrier Proteins genetics
- Abstract
Cullin (CUL)-dependent ubiquitin ligases form a class of structurally related multisubunit enzymes that control the rapid and selective degradation of important regulatory proteins involved in cell cycle progression and development, among others. The CUL3-BTB ligases belong to this class of enzymes and despite recent findings on their molecular composition, our knowledge on their functions and substrates remains still very limited. In contrast to budding and fission yeast, CUL3 is an essential gene in metazoans. The model plant Arabidopsis thaliana encodes two related CUL3 genes, called CUL3A and CUL3B. We recently reported that cul3a loss-of-function mutants are viable but exhibit a mild flowering and light sensitivity phenotype. We investigated the spatial and temporal expression of the two CUL3 genes in reproductive tissues and found that their expression patterns are largely overlapping suggesting possible functional redundancy. Thus, we investigated the consequences on plant development of combined Arabidopsis cul3a cul3b loss-of-function mutations. Homozygous cul3b mutant plants developed normally and were fully fertile. However, the disruption of both the CUL3A and CUL3B genes reduced gametophytic transmission and caused embryo lethality. The observed embryo abortion was found to be under maternal control. Arrest of embryogenesis occurred at multiple stages of embryo development, but predominantly at the heart stage. At the cytological level, CUL3 loss-of-function mutations affected both embryo pattern formation and endosperm development.
- Published
- 2005
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34. Two waves of programmed cell death occur during formation and development of somatic embryos in the gymnosperm, Norway spruce.
- Author
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Filonova LH, Bozhkov PV, Brukhin VB, Daniel G, Zhivotovsky B, and von Arnold S
- Subjects
- DNA Fragmentation, DNA, Plant, Apoptosis, Trees embryology, Trees genetics
- Abstract
In the animal life cycle, the earliest manifestations of programmed cell death (PCD) can already be seen during embryogenesis. The aim of this work was to determine if PCD is also involved in the elimination of certain cells during plant embryogenesis. We used a model system of Norway spruce somatic embryogenesis, which represents a multistep developmental pathway with two broad phases. The first phase is represented by proliferating proembryogenic masses (PEMs). The second phase encompasses development of somatic embryos, which arise from PEMs and proceed through the same sequence of stages as described for their zygotic counterparts. Here we demonstrate two successive waves of PCD, which are implicated in the transition from PEMs to somatic embryos and in correct embryonic pattern formation, respectively. The first wave of PCD is responsible for the degradation of PEMs when they give rise to somatic embryos. We show that PCD in PEM cells and embryo formation are closely interlinked processes, both stimulated upon withdrawal or partial depletion of auxins and cytokinins. The second wave of PCD eliminates terminally differentiated embryo-suspensor cells during early embryogeny. During the dismantling phase of PCD, PEM and embryo-suspensor cells exhibit progressive autolysis, resulting in the formation of a large central vacuole. Autolytic degradation of the cytoplasm is accompanied by lobing and budding-like segmentation of the nucleus. Nuclear DNA undergoes fragmentation into both large fragments of about 50 kb and multiples of approximately 180 bp. The tonoplast rupture is delayed until lysis of the cytoplasm and organelles, including the nucleus, is almost complete. The protoplasm then disappears, leaving a cellular corpse represented by only the cell wall. This pathway of cell dismantling suggests overlapping of apoptotic and autophagic types of PCD during somatic embryogenesis in Norway spruce.
- Published
- 2000
- Full Text
- View/download PDF
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