31 results on '"Kryvokhyzha, Dmytro"'
Search Results
2. RNA sequencing unravels novel L cell constituents and mechanisms of GLP-1 secretion in human gastric bypass-operated intestine
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Miskelly, Michael G., Lindqvist, Andreas, Piccinin, Elena, Hamilton, Alexander, Cowan, Elaine, Nergård, Bent-Johnny, Del Giudice, Rita, Ngara, Mtakai, Cataldo, Luis R., Kryvokhyzha, Dmytro, Volkov, Petr, Engelking, Luke, Artner, Isabella, Lagerstedt, Jens O., Eliasson, Lena, Ahlqvist, Emma, Moschetta, Antonio, Hedenbro, Jan, and Wierup, Nils
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- 2024
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3. GPR162 is a beta cell CART receptor
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Lindqvist, Andreas, Abels, Mia, Shcherbina, Liliya, Ngara, Mtakai, Kryvokhyzha, Dmytro, Chriett, Sabrina, Riva, Matteo, Fajul, Abul, Barghouth, Mohammad, Luan, Cheng, Eliasson, Lena, Larsen, Olav, Rosenkilde, Mette M., Zhang, Enming, Renström, Erik, and Wierup, Nils
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- 2023
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4. Cryptic expansion of hybrid polyploid spined loaches Cobitis in the rivers of Eastern Europe
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Mezhzherin, Sergey V., Tsyba, Anton A., and Kryvokhyzha, Dmytro
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- 2022
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5. Short-term lingonberry feeding is associated with decreased insulin levels and altered adipose tissue function in high-fat diet fed C57BL/6J mice
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Kotowska, Dorota, Neuhaus, Mathis, Heyman-Lindén, Lovisa, Morén, Björn, Li, Shuyi, Kryvokhyzha, Dmytro, Berger, Karin, and Stenkula, Karin G
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- 2022
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6. High-throughput muscle fiber typing from RNA sequencing data
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Oskolkov, Nikolay, Santel, Malgorzata, Parikh, Hemang M., Ekström, Ola, Camp, Gray J., Miyamoto-Mikami, Eri, Ström, Kristoffer, Mir, Bilal Ahmad, Kryvokhyzha, Dmytro, Lehtovirta, Mikko, Kobayashi, Hiroyuki, Kakigi, Ryo, Naito, Hisashi, Eriksson, Karl-Fredrik, Nystedt, Björn, Fuku, Noriyuki, Treutlein, Barbara, Pääbo, Svante, and Hansson, Ola
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- 2022
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7. Myocardin regulates exon usage in smooth muscle cells through induction of splicing regulatory factors
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Liu, Li, Kryvokhyzha, Dmytro, Rippe, Catarina, Jacob, Aishwarya, Borreguero-Muñoz, Andrea, Stenkula, Karin G., Hansson, Ola, Smith, Christopher W. J., Fisher, Steven A., and Swärd, Karl
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- 2022
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8. Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris) - DATA
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Kryvokhyzha, Dmytro
- Abstract
Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C.bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to follow similar trajectories and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allotetraploid C.bursa-pastoris and its parental species, the outcrossing C.grandiflora and the self-fertilizing C.orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C.orientalis and expression in root and leaf to that of C.grandiflora. Since deleterious mutations accumulated preferentially on the C.orientalis subgenome, the bias in expression towards C.orientalis observed in flowers indicates that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C.grandiflora subgenome may be reflective of the differential genetic load.
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- 2022
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9. Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae) - DATA
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Kryvokhyzha, Dmytro
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transcriptomics ,SIFT ,allopolyploidy ,gene expression ,genetic load ,admixture ,selection ,genome evolution ,demographic history ,nwk ,SIFT4G ,SNPs - Abstract
Data associated with the paper. Abstract: Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg . There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions.
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- 2022
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10. How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus
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Zhang, Zebin, primary, Kryvokhyzha, Dmytro, additional, Orsucci, Marion, additional, Glémin, Sylvain, additional, Milesi, Pascal, additional, and Lascoux, Martin, additional
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- 2022
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11. The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe
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Cornille, Amandine, primary, Tiret, Mathieu, additional, Salcedo, Adriana, additional, Huang, Huirun R, additional, Orsucci, Marion, additional, Milesi, Pascal, additional, Kryvokhyzha, Dmytro, additional, Holm, Karl, additional, Ge, Xue-Jun, additional, Stinchcombe, John R, additional, Glémin, Sylvain, additional, Wright, Stephen I, additional, and Lascoux, Martin, additional
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- 2022
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12. Additional file 1 of High-throughput muscle fiber typing from RNA sequencing data
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Oskolkov, Nikolay, Santel, Malgorzata, Parikh, Hemang M., Ekström, Ola, Camp, Gray J., Miyamoto-Mikami, Eri, Ström, Kristoffer, Mir, Bilal Ahmad, Kryvokhyzha, Dmytro, Lehtovirta, Mikko, Kobayashi, Hiroyuki, Kakigi, Ryo, Naito, Hisashi, Eriksson, Karl-Fredrik, Nystedt, Björn, Fuku, Noriyuki, Treutlein, Barbara, Pääbo, Svante, and Hansson, Ola
- Abstract
Additional file 1: Figure S1. Seurat snRNAseq workflow quality control statistics. From left to right, first figure reports the number of expressed genes per cell, second figure reports the number of UMIs (library size) per cell, third figure shows the fraction of reads mapped to mitochondrial genes per cell. Figure S2. The initial average sequencing depth of 35 million paired-end (PE) reads were ´down-sampled´ and mean square errors between the ATPase and totRNAseq predicted fractions of Type I fibers were calculated. Figure S3. Principal Component Analysis (PCA) plot of gene exppression from human skeletal muscle snRNAseq colored by the cluster annotation, see Figure 1A, obtained from the Louvain clustering on the number of significant principal components (according to Seurat workflow). Figure S4. (a) Principal Component Analysis (PCA) plot, and (b) tSNE plot of gene expression from human skeletal muscle snRNAseq colored by the cell cycle annotation obtained from the CellCycleScoring function from Seurat workflow. No obvious cluster formation based on the cell cycle can be observed from neither the PCA nor the tSNE plot.
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- 2022
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13. Correction: The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels
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Axelsson, Erik, primary, Ljungvall, Ingrid, additional, Bhoumik, Priyasma, additional, Conn, Laura Bas, additional, Muren, Eva, additional, Ohlsson, Åsa, additional, Olsen, Lisbeth Høier, additional, Engdahl, Karolina, additional, Hagman, Ragnvi, additional, Hanson, Jeanette, additional, Kryvokhyzha, Dmytro, additional, Pettersson, Mats, additional, Grenet, Olivier, additional, Moggs, Jonathan, additional, Rio-Espinola, Alberto Del, additional, Epe, Christian, additional, Taillon, Bruce, additional, Tawari, Nilesh, additional, Mane, Shrinivas, additional, Hawkins, Troy, additional, Hedhammar, Åke, additional, Gruet, Philippe, additional, Häggström, Jens, additional, and Lindblad-Toh, Kerstin, additional
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- 2022
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14. High-Throughput Muscle Fiber Typing From RNA Sequencing Data
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Oskolkov, Nikolay, primary, Santel, Malgorzata, additional, Ekström, Ola, additional, Camp, Gray J., additional, Miyamoto-Mikami, Eri, additional, Ström, Kristoffer, additional, Parikh, Hemang M., additional, Mir, Bilal, additional, Kryvokhyzha, Dmytro, additional, Lehtovirta, Mikko, additional, Kobayashi, Hiroyuki, additional, Kakigi, Ryo, additional, Naito, Hisashi, additional, Eriksson, Karl-Fredrik, additional, Nystedt, Björn, additional, Fuku, Noriyuki, additional, Treutlein, Barbara, additional, Pääbo, Svante, additional, and Hansson, Ola, additional
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- 2021
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15. Regulation of the Muscarinic M3 Receptor by Myocardin-Related Transcription Factors
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Liu, Li, primary, Rippe, Catarina, additional, Hansson, Ola, additional, Kryvokhyzha, Dmytro, additional, Fisher, Steven, additional, Ekman, Mari, additional, and Swärd, Karl, additional
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- 2021
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16. The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels
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Axelsson, Erik, primary, Ljungvall, Ingrid, additional, Bhoumik, Priyasma, additional, Conn, Laura Bas, additional, Muren, Eva, additional, Ohlsson, Åsa, additional, Olsen, Lisbeth Høier, additional, Engdahl, Karolina, additional, Hagman, Ragnvi, additional, Hanson, Jeanette, additional, Kryvokhyzha, Dmytro, additional, Pettersson, Mats, additional, Grenet, Olivier, additional, Moggs, Jonathan, additional, Del Rio-Espinola, Alberto, additional, Epe, Christian, additional, Taillon, Bruce, additional, Tawari, Nilesh, additional, Mane, Shrinivas, additional, Hawkins, Troy, additional, Hedhammar, Åke, additional, Gruet, Philippe, additional, Häggström, Jens, additional, and Lindblad-Toh, Kerstin, additional
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- 2021
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17. Genetic variation at RAB3GAP2 and its role in exercise-related adaptation and recovery
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Ström, Kristoffer, primary, Oskolkov, Nikolay, additional, Karaderi, Tugce, additional, Kalamajski, Sebastian, additional, Ekström, Ola, additional, Miyamoto-Mikami, Eri, additional, Ladenvall, Claes, additional, Kakulidis, Ellen, additional, Reid, Steven, additional, Andersson, Anna-Maria Dutius, additional, Kryvokhyzha, Dmytro, additional, Zhang, Enming, additional, Fadista, João, additional, Iemitsu, Motoyuki, additional, Mahajan, Anubha, additional, Ahlqvist, Emma, additional, Prasad, Rashmi, additional, Pruefer, Kay, additional, Sabater-Lleal, Maria, additional, Smith, Nicholas, additional, Dehghan, Abbas Abbas, additional, Lind, Lars, additional, McGawley, Kerry, additional, Morris, Andrew, additional, Lehtovirta, Mikko, additional, Szczerbiński, Łukasz, additional, Kretowski, Adam, additional, Wang, Guan, additional, Pitsiladis, Yannis, additional, Santos-Lozano, Alejandro, additional, Lucia, Alejandro, additional, Fuku, Noriyuku, additional, Holmberg, Hans-Christer, additional, Groop, Leif, additional, Gomez, Maria, additional, Eriksson, Karl-Fredrik, additional, Pietras, Kristian, additional, Lindgren, Cecilia, additional, Franks, Paul, additional, and Hansson, Ola, additional
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- 2021
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18. relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe.
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Cornille, Amandine, Tiret, Mathieu, Salcedo, Adriana, Huang, Huirun R, Orsucci, Marion, Milesi, Pascal, Kryvokhyzha, Dmytro, Holm, Karl, Ge, Xue-Jun, Stinchcombe, John R, Glémin, Sylvain, Wright, Stephen I, and Lascoux, Martin
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GARDENS ,PHENOTYPIC plasticity ,LIFE history theory ,COLONIZATION (Ecology) ,PHENOTYPES ,WEEDS - Abstract
The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative contributions of plasticity, performance and demographic history to the worldwide expansion of the shepherd's purse, Capsella bursa-pastoris. We installed two large common gardens of the shepherd's purse, a young, self-fertilizing, allopolyploid weed with a worldwide distribution. One common garden was located in Europe, the other in Asia. We used accessions from three distinct genetic clusters (Middle East, Europe and Asia) that reflect the demographic history of the species. Several life-history traits were measured. To explain the phenotypic variation between and within genetic clusters, we analysed the effects of (i) the genetic clusters, (ii) the phenotypic plasticity and its association to fitness and (iii) the distance in terms of bioclimatic variables between the sampling site of an accession and the common garden, i.e. the environmental distance. Our experiment showed that (i) the performance of C. bursa-pastoris is closely related to its high phenotypic plasticity; (ii) within a common garden, genetic cluster was a main determinant of phenotypic differences; and (iii) at the scale of the experiment, the effect of environmental distance to the common garden could not be distinguished from that of genetic clusters. Phenotypic plasticity and demographic history both play important role at different stages of range expansion. The success of the worldwide expansion of C. bursa-pastoris was undoubtedly influenced by its strong phenotypic plasticity. [ABSTRACT FROM AUTHOR]
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- 2022
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19. Fifteen shades of green: The evolution of Bufotes toads revisited
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Dufresnes, Christophe, primary, Mazepa, Glib, additional, Jablonski, Daniel, additional, Oliveira, Ricardo Caliari, additional, Wenseleers, Tom, additional, Shabanov, Dmytro A., additional, Auer, Markus, additional, Ernst, Raffael, additional, Koch, Claudia, additional, Ramírez-Chaves, Héctor E., additional, Mulder, Kevin Patrick, additional, Simonov, Evgeniy, additional, Tiutenko, Arthur, additional, Kryvokhyzha, Dmytro, additional, Wennekes, Paul L., additional, Zinenko, Oleksandr I., additional, Korshunov, Oleksiy V., additional, Al-Johany, Awadh M., additional, Peregontsev, Evgeniy A., additional, Masroor, Rafaqat, additional, Betto-Colliard, Caroline, additional, Denoël, Mathieu, additional, Borkin, Leo J., additional, Skorinov, Dmitriy V., additional, Pasynkova, Roza A., additional, Mazanaeva, Lyudmila F., additional, Rosanov, Juriy M., additional, Dubey, Sylvain, additional, and Litvinchuk, Spartak, additional
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- 2019
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20. Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
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Kryvokhyzha, Dmytro, Salcedo, Adriana, Eriksson, Mimmi C., Duan, Tianlin, Tawari, Nilesh, Chen, Jun, Guerrina, Maria, Kreiner, Julia M., Kent, Tyler V., Lagercrantz, Ulf, Stinchcombe, John R., Glémin, Sylvain, Wright, Stephen I., Lascoux, Martin, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Department of Ecology and Evolutionary Biology [University of Toronto] (EEB), University of Toronto, Department of Biological and Environmental Sciences [Gothenburg], University of Gothenburg (GU), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Vetenskapsrådet, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
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Gene Flow ,Viral Diseases ,Computer and Information Sciences ,Heredity ,Asia ,DNA, Plant ,lcsh:QH426-470 ,Gene Expression ,Geographical Locations ,Polyploidy ,Evolution, Molecular ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,Evolutionsbiologi ,Middle East ,Species Specificity ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Medicine and Health Sciences ,Genetics ,Evolutionary Systematics ,Capsella ,Rubella ,Phylogeny ,Taxonomy ,Data Management ,Evolutionary Biology ,[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,Population Biology ,Models, Genetic ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,Biology and Life Sciences ,Phylogenetic Analysis ,Diploidy ,Phylogenetics ,Europe ,Tetraploidy ,Phylogeography ,lcsh:Genetics ,Infectious Diseases ,Deletion Mutation ,Genetics, Population ,People and Places ,Mutation ,Hybridization, Genetic ,Departures from Diploidy ,Population Genetics ,Genome, Plant ,Research Article - Abstract
Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg. There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions., Author summary Allopolyploid species have two or more sets of chromosomes that originate from hybridization of different species. It remains largely unknown how the two genomes evolve in the same organism and how strongly their evolutionary trajectory depends on the initial differences between the two parental species and the specific demographic history of the newly formed allopolyploid species. To address these questions, we analyzed the genomic and gene expression variation of the shepherd’s purse, a recent allopolyploid species, in three regions of its natural range. After ∼100,000 generations of co-existence within the same species, the two subgenomes had still retained part of the initial difference between the two parental species in the number of deleterious mutations reflecting a history of mating system differences. This difference, as well as differences in patterns of positive selection and levels of gene expression, also strongly depended on the specific histories of the three regions considered. Most strikingly, and unexpectedly, the allopolyploid species showed signs of hybridization with different diploid relatives or multiple origins in different parts of its range. Regardless if it was hybridization or multiple origins, this profoundly altered the relationship between the two subgenomes in different regions. Hence, our study illustrates how both the genomic structure and ecological arena interact to determine the evolutionary trajectories of allopolyploid species.
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- 2019
21. Regulation of the Muscarinic M3 Receptor by Myocardin-Related Transcription Factors.
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Liu, Li, Rippe, Catarina, Hansson, Ola, Kryvokhyzha, Dmytro, Fisher, Steven, Ekman, Mari, and Swärd, Karl
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MUSCARINIC receptors ,TRANSCRIPTION factors ,SERUM response factor ,CARBACHOL ,CELL receptors ,MUSCARINIC agonists - Abstract
Myocardin-related transcription factors (MRTFs: myocardin/ MYOCD , MRTF-A/ MRTFA , and MRTF-B/ MRTFB) are co-factors of serum response factor (SRF) that activate the smooth muscle cell (SMC) gene program and that play roles in cardiovascular development and mechanobiology. Gain and loss of function experiments have defined the SMC gene program under control of MRTFs, yet full understanding of their impact is lacking. In the present study, we tested the hypothesis that the muscarinic M
3 receptor (CHRM3) is regulated by MRTFs together with SRF. Forced expression of MYOCD (8d) in human coronary artery (SMC) followed by RNA-sequencing showed increased levels of M2 , M3 , and M5 receptors (CHRM2 : 2-fold, CHRM3 : 16-fold, and CHRM5 : 2-fold). The effect of MYOCD on M3 was confirmed by RT-qPCR using both coronary artery and urinary bladder SMCs, and correlation analyses using human transcriptomic datasets suggested that M3 may also be regulated by MRTF-B. Head-to-head comparisons of MYOCD, MRTF-A and MRTF-B, argued that while all MRTFs are effective, MRTF-B is the most powerful transactivator of CHRM3 , causing a 600-fold increase at 120h. Accordingly, MRTF-B conferred responsiveness to the muscarinic agonist carbachol in Ca2+ imaging experiments. M3 was suppressed on treatment with the MRTF-SRF inhibitor CCG-1423 using SMCs transduced with either MRTF-A or MRTF-B and using intact mouse esophagus in culture (by 92±2%). Moreover, silencing of SRF with a short hairpin reduced CHRM3 (by >60%) in parallel with α-actin (ACTA2). Tamoxifen inducible knockout of Srf in smooth muscle reduced Srf (by 54±4%) and Chrm3 (by 41±6%) in the urinary bladder at 10days, but Srf was much less reduced or unchanged in aorta, ileum, colon, trachea, and esophagus. Longer induction (21d) further accentuated the reduction of Chrm3 in the bladder and ileum, but no change was seen in the aorta. Single cell RNA-sequencing revealed that Mrtfb dominates in ECs, while Myocd dominates in SMCs, raising the possibility that Chrm3 may be driven by Mrtfb-Srf in the endothelium and by Myocd-Srf in SMCs. These findings define a novel transcriptional control mechanism for muscarinic M3 receptors in human cells, and in mice, that could be targeted for therapy. [ABSTRACT FROM AUTHOR]- Published
- 2021
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22. Genome evolution and adaptation of a successful allopolyploid, Capsella bursa-pastoris
- Author
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Kryvokhyzha, Dmytro
- Subjects
Evolutionsbiologi ,Evolutionary Biology ,gene expression ,genetic load ,selection ,population structure ,parental legacy ,genetic drift ,allopolyploidy - Abstract
The term allopolyploid refers to an organism that originated through hybridization and increased its ploidy level by retaining the unreduced genomes of its parents. Both hybridization and polyploidy usually have negative consequences for the organism. However, there are species that not only survive these modifications but even thrive and can outcompete their diploid relatives. There are many intuitive explanations for the success of polyploids, but the number of empirical studies is limited. The shepherd's purse (Capsella bursa-pastoris) is an emerging model for studying a successful allopolyploid species. C. bursa-pastoris occurs worldwide, whereas its parental species, Capsella grandiflora and Capsella orientalis, have more limited distribution range. C. grandiflora is confined to Northern Greece and Albania, and C. orientalis is found only in the steppes of Central Asia. We described the genetic variation within C. bursa-pastoris and showed that it is not homogeneous across Eurasia but rather subdivided into three genetically distinct populations: one comprises accessions from Europe and Eastern Siberia, the second one is located in Eastern Asia and the third one groups accessions around the Middle East. Reconstruction of the colonization history suggested that this species originated in the Middle East and subsequently spread to Europe and Eastern Asia. This colonization was probably human-mediated. Interestingly, these three populations survive in different environmental conditions, and yet most gene expression differences between them could be explained by neutral processes. We also found that despite a common history within one species, the two subgenomes retained differences already present between the parental species. In particular, the genetic load was still higher on the subgenome inherited from C. orientalis than on the one inherited from C. grandiflora. The two subgenomes were also differentially influenced by introgression and selection in the three genetic clusters. Gene expression variation was highly correlated between the two subgenomes but the total level of expression showed variation in parental dominance across flower, leaf, and root tissues. This thesis for the first time shows that the evolutionary pathways of allopolyploids may differ not only on the species level but also between populations within one species. It also supports the theory that alloploidy provides an increased amount of genetic material that enables evolutionary flexibility.
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- 2018
23. Variation in competitive ability with mating system, ploidy and range expansion in four Capsella species
- Author
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Glémin, Sylvain, Yang, Xuyue, Petrone-Mendoza, Sandra, Hansen, Johanna, ORSUCCI, MARION, Kryvokhyzha, Dmytro, Duan, Tianlin, Milesi, P., Lascoux, Martin, Briand, Valerie, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Department of Ecology, Environment and Plant Sciences, Stockholm University, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Uppsala University, Department of Ecology and Genetics [Uppsala] (EBC), SFEcologie, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Stockholm University, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), and Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
24. Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)
- Author
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Kryvokhyzha, Dmytro, primary, Milesi, Pascal, additional, Duan, Tianlin, additional, Orsucci, Marion, additional, Wright, Stephen I., additional, Glémin, Sylvain, additional, and Lascoux, Martin, additional
- Published
- 2019
- Full Text
- View/download PDF
25. Towards the new normal: Transcriptomic and genomic changes in the two subgenomes of a 100,000 years old allopolyploid, Capsella bursa-pastoris
- Author
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Kryvokhyzha, Dmytro, primary, Milesi, Pascal, additional, Duan, Tianlin, additional, Orsucci, Marion, additional, Wright, Stephen I., additional, Glémin, Sylvain, additional, and Lascoux, Martin, additional
- Published
- 2018
- Full Text
- View/download PDF
26. Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
- Author
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Kryvokhyzha, Dmytro, primary, Salcedo, Adriana, additional, Eriksson, Mimmi C., additional, Duan, Tianlin, additional, Tawari, Nilesh, additional, Chen, Jun, additional, Guerrina, Maria, additional, Kreiner, Julia M., additional, Kent, Tyler V., additional, Lagercrantz, Ulf, additional, Stinchcombe, John R., additional, Glémin, Sylvain, additional, Wright, Stephen I., additional, and Lascoux, Martin, additional
- Published
- 2017
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- View/download PDF
27. Integrative Transcriptome and Proteome Profiling of Insulin-Resistant Kidney Cell Models and Patient Biopsies Reveals Common and Cell Type-Specific Mechanisms Underpinning Diabetic Kidney Disease
- Author
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Coward, Richard, Lay, Abigail C., Tran, Van Du T., Nair, Viji, Betin, Virginie M., Burdet, Frédéric, Mehl, Florence, Kryvokhyzha, Dmytro, Ahmad, Abrar, Lewis, Philip A., Wilson, Marieangela C., Menon, Rajasree, Otto, Edgar A., Heesom, Kate J., Looker, Helen C., Nelson, Robert G., Ju, Wenjun, Kretzler, Matthias, Satchell, Simon C., and Gomez, Maria F.
- Published
- 2023
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28. The influence of population structure on gene expression and flowering time variation in the ubiquitous weedCapsella bursa-pastoris(Brassicaceae)
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Kryvokhyzha, Dmytro, primary, Holm, Karl, additional, Chen, Jun, additional, Cornille, Amandine, additional, Glémin, Sylvain, additional, Wright, Stephen I., additional, Lagercrantz, Ulf, additional, and Lascoux, Martin, additional
- Published
- 2016
- Full Text
- View/download PDF
29. The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae).
- Author
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Kryvokhyzha, Dmytro, Holm, Karl, Chen, Jun, Cornille, Amandine, Glémin, Sylvain, Wright, Stephen I., Lagercrantz, Ulf, and Lascoux, Martin
- Subjects
- *
GENE expression , *FLOWERING time , *CAPSELLA , *BRASSICACEAE , *CIRCADIAN rhythms , *PLANTS - Abstract
Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing ( GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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- View/download PDF
30. Regulation of the Muscarinic M 3 Receptor by Myocardin-Related Transcription Factors.
- Author
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Liu L, Rippe C, Hansson O, Kryvokhyzha D, Fisher S, Ekman M, and Swärd K
- Abstract
Myocardin-related transcription factors (MRTFs: myocardin/ MYOCD , MRTF-A/ MRTFA , and MRTF-B/ MRTFB ) are co-factors of serum response factor (SRF) that activate the smooth muscle cell (SMC) gene program and that play roles in cardiovascular development and mechanobiology. Gain and loss of function experiments have defined the SMC gene program under control of MRTFs, yet full understanding of their impact is lacking. In the present study, we tested the hypothesis that the muscarinic M
3 receptor ( CHRM3 ) is regulated by MRTFs together with SRF. Forced expression of MYOCD (8d) in human coronary artery (SMC) followed by RNA-sequencing showed increased levels of M2 , M3 , and M5 receptors ( CHRM2 : 2-fold, CHRM3 : 16-fold, and CHRM5 : 2-fold). The effect of MYOCD on M3 was confirmed by RT-qPCR using both coronary artery and urinary bladder SMCs, and correlation analyses using human transcriptomic datasets suggested that M3 may also be regulated by MRTF-B. Head-to-head comparisons of MYOCD, MRTF-A and MRTF-B, argued that while all MRTFs are effective, MRTF-B is the most powerful transactivator of CHRM3 , causing a 600-fold increase at 120h. Accordingly, MRTF-B conferred responsiveness to the muscarinic agonist carbachol in Ca2+ imaging experiments. M3 was suppressed on treatment with the MRTF-SRF inhibitor CCG-1423 using SMCs transduced with either MRTF-A or MRTF-B and using intact mouse esophagus in culture (by 92±2%). Moreover, silencing of SRF with a short hairpin reduced CHRM3 (by >60%) in parallel with α-actin ( ACTA2 ). Tamoxifen inducible knockout of Srf in smooth muscle reduced Srf (by 54±4%) and Chrm3 (by 41±6%) in the urinary bladder at 10days, but Srf was much less reduced or unchanged in aorta, ileum, colon, trachea, and esophagus. Longer induction (21d) further accentuated the reduction of Chrm3 in the bladder and ileum, but no change was seen in the aorta. Single cell RNA-sequencing revealed that Mrtfb dominates in ECs, while Myocd dominates in SMCs, raising the possibility that Chrm3 may be driven by Mrtfb-Srf in the endothelium and by Myocd-Srf in SMCs. These findings define a novel transcriptional control mechanism for muscarinic M3 receptors in human cells, and in mice, that could be targeted for therapy., (Copyright © 2021 Liu, Rippe, Hansson, Kryvokhyzha, Fisher, Ekman and Swärd.)- Published
- 2021
- Full Text
- View/download PDF
31. Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae).
- Author
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Kryvokhyzha D, Salcedo A, Eriksson MC, Duan T, Tawari N, Chen J, Guerrina M, Kreiner JM, Kent TV, Lagercrantz U, Stinchcombe JR, Glémin S, Wright SI, and Lascoux M
- Subjects
- Asia, Capsella classification, DNA, Plant genetics, Diploidy, Europe, Genetics, Population, Hybridization, Genetic, Middle East, Models, Genetic, Mutation, Phylogeny, Phylogeography, Polyploidy, Species Specificity, Capsella genetics, Evolution, Molecular, Genome, Plant, Tetraploidy
- Abstract
Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg. There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2019
- Full Text
- View/download PDF
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