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Your search keyword '"Nizhynska, Viktoria"' showing total 16 results
Start Over Author "Nizhynska, Viktoria" Publisher mittuniversitetet, avdelningen for naturvetenskap
16 results on '"Nizhynska, Viktoria"'

1. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica

Author

Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, Nordborg, Magnus, Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, and Nordborg, Magnus

Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

Published
2017
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2. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica

Author

Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, Nordborg, Magnus, Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, and Nordborg, Magnus

Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

Published
2017
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3. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica

Author

Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, Nordborg, Magnus, Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, and Nordborg, Magnus

Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

Published
2017
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4. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica

Author

Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, Nordborg, Magnus, Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, and Nordborg, Magnus

Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

Published
2017
Full Text
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5. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica

Author

Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, Nordborg, Magnus, Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, and Nordborg, Magnus

Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

Published
2017
Full Text
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6. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica

Author

Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, Nordborg, Magnus, Novikova, Polina Yu, Tsuchimatsu, Takashi, Simon, Samson, Nizhynska, Viktoria, Voronin, Viktor, Burns, Robin, Fedorenko, Olga M., Holm, Svante, Saell, Torbjoern, Prat, Elisa, Marande, William, Castric, Vincent, and Nordborg, Magnus

Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

Published
2017
Full Text
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7. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Schork, Nicholas J., Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, and Schork, Nicholas J.

Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Published
2016
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8. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Abstract

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Published
2016
Full Text
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9. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Abstract

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Published
2016
Full Text
View/download PDF

10. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Schork, Nicholas J., Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, and Schork, Nicholas J.

Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Published
2016
Full Text
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11. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Schork, Nicholas J., Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, and Schork, Nicholas J.

Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Published
2016
Full Text
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12. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Abstract

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Published
2016
Full Text
View/download PDF

13. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Abstract

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Published
2016
Full Text
View/download PDF

14. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Schork, Nicholas J., Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, and Schork, Nicholas J.

Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Published
2016
Full Text
View/download PDF

15. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Schork, Nicholas J., Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J., Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, and Schork, Nicholas J.

Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Published
2016
Full Text
View/download PDF

16. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Abstract

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Published
2016
Full Text
View/download PDF

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