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4. Establishment and stability of the latent HIV-1 DNA reservoir

Author

Brodin, Johanna, Zanini, Fabio, Thebo, Lina, Lanz, Christa, Bratt, Göran, Neher, Richard A., and Albert, Jan

Subjects
Quantitative Biology - Populations and Evolution
Abstract

HIV-1 infection currently cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). To characterize establishment, turnover, and evolution of viral DNA reservoirs we deep-sequenced the p17gag region of the HIV-1 genome from samples obtained after 3-18 years of suppressive ART from 10 patients. For each of these patients, whole genome deep-sequencing data of HIV-1 RNA populations before onset of ART were available from 6-12 longitudinal plasma samples spanning 5-8 years of untreated infection. This enabled a detailed analysis of the dynamics and origin of proviral DNA during ART. A median of 14% (range 0-42%) of the p17gag DNA sequences were overtly defective due to G-to-A hypermutation. The remaining sequences were remarkably similar to previously observed RNA sequences and showed no evidence of evolution over many years of suppressive ART. Most sequences from the DNA reservoirs were very similar to viruses actively replicating in plasma (RNA sequences) shortly before start of ART. The results do not support persistent HIV-1 replication as a mechanism to maintain the HIV-1 reservoir during suppressive therapy. Rather, the data indicate that viral DNA variants are turning over as long as patients are untreated and that suppressive ART halts this turnover.

Published
2016

5. Population genomics of intrapatient HIV-1 evolution

Author

Zanini, Fabio, Brodin, Johanna, Thebo, Lina, Lanz, Christa, Bratt, Göran, Albert, Jan, and Neher, Richard A.

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity.

Published
2015
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6. Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

Author

Calderón, Luciano, primary, Carbonell-Bejerano, Pablo, additional, Muñoz, Claudio, additional, Bree, Laura, additional, Sola, Cristobal, additional, Bergamin, Daniel, additional, Tulle, Walter, additional, Gomez-Talquenca, Sebastian, additional, Lanz, Christa, additional, Royo, Carolina, additional, Ibáñez, Javier, additional, Martinez-Zapater, José Miguel, additional, Weigel, Detlef, additional, and Lijavetzky, Diego, additional

Published
2024
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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, Consortium, The 1001 Genomes, 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

Subjects
Human Genome, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Arabidopsis, DNA Methylation, Epigenesis, Genetic, Epigenomics, Gene Expression Regulation, Plant, Genome, Plant, Transcriptome, Genomes Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
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

9. Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

Author

Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Calderón, Luciano [0000-0003-4223-0149], Carbonell-Bejerano, Pablo [0000-0002-7266-9665], Ibáñez, Javier [0000-0002-6286-5638], Lijavetzky, Diego [0000-0003-4207-3067], Calderón, Luciano, Carbonell-Bejerano, Pablo, Muñoz, Claudio, Bree, Laura, Sola, Cristobal, Bergamin, Daniel, Tulle, Walter, Gomez-Talquenca, Sebastian, Lanz, Christa, Royo, Carolina, Ibáñez, Javier, Martinez-Zapater, José Miguel, Weigel, Detlef, Lijavetzky, Diego, Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Calderón, Luciano [0000-0003-4223-0149], Carbonell-Bejerano, Pablo [0000-0002-7266-9665], Ibáñez, Javier [0000-0002-6286-5638], Lijavetzky, Diego [0000-0003-4207-3067], Calderón, Luciano, Carbonell-Bejerano, Pablo, Muñoz, Claudio, Bree, Laura, Sola, Cristobal, Bergamin, Daniel, Tulle, Walter, Gomez-Talquenca, Sebastian, Lanz, Christa, Royo, Carolina, Ibáñez, Javier, Martinez-Zapater, José Miguel, Weigel, Detlef, and Lijavetzky, Diego

Abstract

[EN] To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with a very low haplotype switch-error rate (<0.025). The haplophase alignment identified > 25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as a reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated with abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and unveil the molecular bases of clonal phenotypic variation.

Published
2024

10. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Author

Yoshida, Kentaro, Schuenemann, Verena J., Cano, Liliana M., Pais, Marina, Mishra, Bagdevi, Sharma, Rahul, Lanz, Christa, Martin, Frank N., Kamoun, Sophien, Krause, Johannes, Thines, Marco, Weigel, Detlef, and Burbano, Hernán A.

Subjects
Quantitative Biology - Genomics
Abstract

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the nineteenth century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the twentieth century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity., Comment: To be published in eLIFE

Published
2013
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11. The genome of the stress-tolerant wild tomato species Solanum pennellii.

Author

Bolger, Anthony, Scossa, Federico, Bolger, Marie E, Lanz, Christa, Maumus, Florian, Tohge, Takayuki, Quesneville, Hadi, Alseekh, Saleh, Sørensen, Iben, Lichtenstein, Gabriel, Fich, Eric A, Conte, Mariana, Keller, Heike, Schneeberger, Korbinian, Schwacke, Rainer, Ofner, Itai, Vrebalov, Julia, Xu, Yimin, Osorio, Sonia, Aflitos, Saulo Alves, Schijlen, Elio, Jiménez-Goméz, José M, Ryngajllo, Malgorzata, Kimura, Seisuke, Kumar, Ravi, Koenig, Daniel, Headland, Lauren R, Maloof, Julin N, Sinha, Neelima, van Ham, Roeland CHJ, Lankhorst, René Klein, Mao, Linyong, Vogel, Alexander, Arsova, Borjana, Panstruga, Ralph, Fei, Zhangjun, Rose, Jocelyn KC, Zamir, Dani, Carrari, Fernando, Giovannoni, James J, Weigel, Detlef, Usadel, Björn, and Fernie, Alisdair R

Subjects
Chromosomes, Plant, Solanum, DNA Transposable Elements, Chromosome Mapping, Genome, Plant, Quantitative Trait Loci, Stress, Physiological, Chromosomes, Plant, Genome, Stress, Physiological, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.

Published
2014

13. Paleocene origin of a streamlined digestive symbiosis in leaf beetles

Author

García-Lozano, Marleny, primary, Henzler, Christine, additional, Porras, Miguel Ángel González, additional, Pons, Inès, additional, Berasategui, Aileen, additional, Lanz, Christa, additional, Budde, Heike, additional, Oguchi, Kohei, additional, Matsuura, Yu, additional, Pauchet, Yannick, additional, Goffredi, Shana, additional, Fukatsu, Takema, additional, Windsor, Donald, additional, and Salem, Hassan, additional

Published
2023
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15. Complete Genome Sequence and Analysis of Wolinella succinogenes

Author

Baar, Claudia, Eppinger, Mark, Raddatz, Guenter, Simon, Jörg, Lanz, Christa, Klimmek, Oliver, Nandakumar, Ramkumar, Gross, Roland, Rosinus, Andrea, Keller, Heike, Jagtap, Pratik, Linke, Burkhard, Meyer, Folker, Lederer, Hermann, and Schuster, Stephan C.

Published
2003

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

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, 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, 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, Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., and Schork, Nicholas J.

Published
2016
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19. 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, and Zhou, Xuefeng

Published
2016
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20. Cycles of satellite and transposon evolution in Arabidopsis centromeres

Author

Wlodzimierz, Piotr, primary, Rabanal, Fernando A., additional, Burns, Robin, additional, Naish, Matthew, additional, Primetis, Elias, additional, Scott, Alison, additional, Mandáková, Terezie, additional, Gorringe, Nicola, additional, Tock, Andrew J., additional, Holland, Daniel, additional, Fritschi, Katrin, additional, Habring, Anette, additional, Lanz, Christa, additional, Patel, Christie, additional, Schlegel, Theresa, additional, Collenberg, Maximilian, additional, Mielke, Miriam, additional, Nordborg, Magnus, additional, Roux, Fabrice, additional, Shirsekar, Gautam, additional, Alonso-Blanco, Carlos, additional, Lysak, Martin A., additional, Novikova, Polina Y., additional, Bousios, Alexandros, additional, Weigel, Detlef, additional, and Henderson, Ian R., additional

Published
2023
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21. Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Author

Kersten, Sonja, primary, Chang, Jiyang, additional, Huber, Christian D., additional, Voichek, Yoav, additional, Lanz, Christa, additional, Hagmaier, Timo, additional, Lang, Patricia, additional, Lutz, Ulrich, additional, Hirschberg, Insa, additional, Lerchl, Jens, additional, Porri, Aimone, additional, Van de Peer, Yves, additional, Schmid, Karl, additional, Weigel, Detlef, additional, and Rabanal, Fernando A., additional

Published
2023
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26. Identificación de variación clonal funcional en Tempranillo y Garnacha mediante el uso de ensamblajes de genomas de referencia varietales

Author

Carbonell-Bejerano, Pablo, Royo, Carolina, Ferradas, Yolanda, Rodríguez-Lorenzo, Maite, Alañón-Sánchez, Noelia, Bezrukov, Ilja, Lanz, Christa, Ibáñez Marcos, Javier, Weigel, Detlef, Martínez-Zapater, José M., European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), and Max Planck Society

Subjects
Ensamblaje de genomas, Tempranillo, Selección clonal, Variación genética somática, Garnacha
Abstract

Trabajo presentado en las IV Jornadas del Grupo de Viticultura de la SECH (Sociedad Española de Ciencias Hortícolas), celebrada en Pamplona (España), del 26 al 28 de octubre de 2022, Las variedades de vid (Vitis vinifera L.) se caracterizan por su alta heterocigosidad (variación entre sus copias genómicas de herencia materna y paterna), lo que obliga a la propagación vegetativa como única vía posible para reproducir su genotipo y sus características varietales. Sin embargo, la propagación vegetativa prolongada da lugar a la acumulación de mutaciones somáticas que en ocasiones pueden producir fenotipos de interés que son la base para la mejora mediante selección clonal. En este trabajo hemos producido ensamblajes de los genomas de Tempranillo y Garnacha. Usando los ensamblajes como referencia, pudimos identificar variación genómica responsable de caracteres de interés en clones o variantes somáticas seleccionadas de cada variedad. En Tempranillo se identificó una deleción de gran tamaño en un clon con color de baya más oscuro de lo normal, relacionada con una reducción en la acumulación de ceras en la cutícula de la baya. En Garnacha se identificaron dos patrones de deleción distintos que causan la pérdida de los genes MYB necesarios para la síntesis de antocianinas en el hollejo, que suponen dos orígenes independientes de la variedad Garnacha Blanca. Estos resultados muestran como el ensamblaje de genoma puede ayudar a conocer el origen de las características varietales y posibilitar la trazabilidad de variación genética clonal útil para la innovación intravarietal., Esta investigación ha sido financiada con fondos EU de la Marie Skłodowska-Curie Individual Fellowship (SomaGrapeGenome 79460) y de los proyectos del Ministerio de Economía (SOMAVID, BIO2014-59324) y del Ministerio de Ciencia e Innovación (DIGEVIDA, PID2020-120183RB-I00), así como con fondos de la ‘Max Planck Society’

Published
2022

29. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Author

Koenig, Daniel, Jiménez-Gómez, José M., Kimura, Seisuke, Fulop, Daniel, Chitwood, Daniel H., Headland, Lauren R., Kumar, Ravi, Covington, Michael F., Devisetty, Upendra Kumar, Tat, An V., Tohge, Takayuki, Bolger, Anthony, Schneeberger, Korbinian, Ossowski, Stephan, Lanz, Christa, Xiong, Guangyan, Taylor-Teeples, Mallorie, Brady, Siobhan M., Pauly, Markus, Weigel, Detlef, Usadel, Björn, Fernie, Alisdair R., Peng, Jie, Sinha, Neelima R., and Maloof, Julin N.

Published
2013

30. A large chimeric deletion associates with impairement of cuticle development in a dark berry somatic variant of Tempranillo Tinto

Author

Carbonell-Bejerano, Pablo, Ferradas, Yolanda, Royo, Carolina, Bezrukov, Ilja, Lanz, Christa, Mauri, Nuria, Alba-Elías, Fernando, Motilva, María-José, Weigel, Detlef, and Martínez-Zapater, José M.

Abstract

Trabajo presentado en el XIII International Symposium on Grapevine Breeding and Genetics, celebrado en Landau in der Pfalz (Alemania), del 10 al 17 de julio de 2022, Color intensity is a relevant feature for red wine quality, which depends on the accumulation of athocyanins during berry ripening and their interaction with other compunds present in the wine. While grape color is a varietal feature, emerging spontaneous somatic variation for this trait can be selected for cultivar improvement. Here we studied the genomic origin of a darker berry clone (VN21) selected in `Tempranillo Tinto¿ (TT) cultivar, which enables the production of wines with higher color intensity. Using a diploid genome assembly of TT produced following a trio binning approach from PacBio and Nanopore sequencing, and genome re-sequencing data of VN21 compared to other TT clones, we identified a 10 Mb deletion in chromosome 11 that likely affected only the L1 meristem cell layer of VN21. An RNA-seq analysis identified a general down-regulation of genes within the chimeric hemizygous segment in the berry skin of VN21. Down-regulated genes where also enriched in wax biosynthesis functional category genes, including one CER1 and one ABCG32 homologs located in the hemizygous segment. SEM images showed that wax accumulation is impaired in the berry cuticle of VN21, which likely leads to the shiny color of VN21 berries. Candidate loss of function polymorphisms remaing hemizygous in VN21 after the chimeric deletion were also detected from TT haplotype comparison. Our findings show that very large hemizygous deletions can stabilize as periclinal chimeras in grapevine clones, giving rise to pleiotropic mutant phenotypes that can be exploited for cultivar innovation.

Published
2022

36. Supplemental material Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Author

Carbonell-Bejerano, Pablo [0000-0002-7266-9665], Nunn, Adam, Rodríguez-Arévalo, Isaac, Tandukar, Zenith, Frels, Katherine, Contreras-Garrido, Andrián, Carbonell-Bejerano, Pablo, Zhang, Panpan, Ramos Cruz, Daniela, Jandrasits, Katharina, Lanz, Christa, Brusa, Anthony, Mirouze, Marie, Dorn, Kevin, Galbraith, David, Jarvis, Brice A., Sedbrook, John C., Wyse, Donald L., Otto, Christian, Langenberger, David, Stadler, Peter F., Weigel, Detlef, Marks, M. David, Anderson, James A., Becker, Claude, Chopra, Ratan, Carbonell-Bejerano, Pablo [0000-0002-7266-9665], Nunn, Adam, Rodríguez-Arévalo, Isaac, Tandukar, Zenith, Frels, Katherine, Contreras-Garrido, Andrián, Carbonell-Bejerano, Pablo, Zhang, Panpan, Ramos Cruz, Daniela, Jandrasits, Katharina, Lanz, Christa, Brusa, Anthony, Mirouze, Marie, Dorn, Kevin, Galbraith, David, Jarvis, Brice A., Sedbrook, John C., Wyse, Donald L., Otto, Christian, Langenberger, David, Stadler, Peter F., Weigel, Detlef, Marks, M. David, Anderson, James A., Becker, Claude, and Chopra, Ratan

Published
2022

37. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Author

Minnesota Department of Agriculture, National Institute of Food and Agriculture (US), Department of Energy (US), Austrian Academy of Sciences, Max Planck Society, European Commission, European Research Council, Federal Ministry of Education and Research (Germany), Nunn, Adam, Rodríguez-Arévalo, Isaac, Tandukar, Zenith, Frels, Katherine, Contreras-Garrido, Andrián, Carbonell-Bejerano, Pablo, Zhang, Panpan, Ramos Cruz, Daniela, Jandrasits, Katharina, Lanz, Christa, Brusa, Anthony, Mirouze, Marie, Dorn, Kevin, Galbraith, David, Jarvis, Brice A., Sedbrook, John C., Wyse, Donald L., Otto, Christian, Langenberger, David, Stadler, Peter F., Weigel, Detlef, Marks, M. David, Anderson, James A., Becker, Claude, Chopra, Ratan, Minnesota Department of Agriculture, National Institute of Food and Agriculture (US), Department of Energy (US), Austrian Academy of Sciences, Max Planck Society, European Commission, European Research Council, Federal Ministry of Education and Research (Germany), Nunn, Adam, Rodríguez-Arévalo, Isaac, Tandukar, Zenith, Frels, Katherine, Contreras-Garrido, Andrián, Carbonell-Bejerano, Pablo, Zhang, Panpan, Ramos Cruz, Daniela, Jandrasits, Katharina, Lanz, Christa, Brusa, Anthony, Mirouze, Marie, Dorn, Kevin, Galbraith, David, Jarvis, Brice A., Sedbrook, John C., Wyse, Donald L., Otto, Christian, Langenberger, David, Stadler, Peter F., Weigel, Detlef, Marks, M. David, Anderson, James A., Becker, Claude, and Chopra, Ratan

Abstract

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

Published
2022

38. Identificación de variación clonal funcional en Tempranillo y Garnacha mediante el uso de ensamblajes de genomas de referencia varietales

Author

European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Max Planck Society, Carbonell-Bejerano, Pablo, Royo, Carolina, Ferradas, Yolanda, Rodríguez-Lorenzo, Maite, Alañón-Sánchez, Noelia, Bezrukov, Ilja, Lanz, Christa, Ibáñez Marcos, Javier, Weigel, Detlef, Martínez-Zapater, José M., European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Max Planck Society, Carbonell-Bejerano, Pablo, Royo, Carolina, Ferradas, Yolanda, Rodríguez-Lorenzo, Maite, Alañón-Sánchez, Noelia, Bezrukov, Ilja, Lanz, Christa, Ibáñez Marcos, Javier, Weigel, Detlef, and Martínez-Zapater, José M.

Abstract

Las variedades de vid (Vitis vinifera L.) se caracterizan por su alta heterocigosidad (variación entre sus copias genómicas de herencia materna y paterna), lo que obliga a la propagación vegetativa como única vía posible para reproducir su genotipo y sus características varietales. Sin embargo, la propagación vegetativa prolongada da lugar a la acumulación de mutaciones somáticas que en ocasiones pueden producir fenotipos de interés que son la base para la mejora mediante selección clonal. En este trabajo hemos producido ensamblajes de los genomas de Tempranillo y Garnacha. Usando los ensamblajes como referencia, pudimos identificar variación genómica responsable de caracteres de interés en clones o variantes somáticas seleccionadas de cada variedad. En Tempranillo se identificó una deleción de gran tamaño en un clon con color de baya más oscuro de lo normal, relacionada con una reducción en la acumulación de ceras en la cutícula de la baya. En Garnacha se identificaron dos patrones de deleción distintos que causan la pérdida de los genes MYB necesarios para la síntesis de antocianinas en el hollejo, que suponen dos orígenes independientes de la variedad Garnacha Blanca. Estos resultados muestran como el ensamblaje de genoma puede ayudar a conocer el origen de las características varietales y posibilitar la trazabilidad de variación genética clonal útil para la innovación intravarietal.

Published
2022

41. Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Author

Nunn, Adam, primary, Rodríguez‐Arévalo, Isaac, additional, Tandukar, Zenith, additional, Frels, Katherine, additional, Contreras‐Garrido, Adrián, additional, Carbonell‐Bejerano, Pablo, additional, Zhang, Panpan, additional, Ramos Cruz, Daniela, additional, Jandrasits, Katharina, additional, Lanz, Christa, additional, Brusa, Anthony, additional, Mirouze, Marie, additional, Dorn, Kevin, additional, Galbraith, David W, additional, Jarvis, Brice A., additional, Sedbrook, John C., additional, Wyse, Donald L., additional, Otto, Christian, additional, Langenberger, David, additional, Stadler, Peter F., additional, Weigel, Detlef, additional, Marks, M. David, additional, Anderson, James A., additional, Becker, Claude, additional, and Chopra, Ratan, additional

Published
2022
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42. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Author

Nunn, Adam, Rodríguez-Arévalo, Isaac, Tandukar, Zenith, Frels, Katherine, Contreras-Garrido, Adrián, Carbonell-Bejerano, Pablo, Zhang, Panpan, Ramos-Cruz, Daniela, Jandrasits, Katharina, Lanz, Christa, Brusa, Anthony, Mirouze, Marie, Dorn, Kevin, Galbraith, David W., Jarvis, Brice A., Sedbrook, John C., Wyse, Donald L., Otto, Christian, Langenberger, David, Stadler, Peter F., Weigel, Detlef, Marks, M. David, Anderson, James A., Becker, Claude, Chopra, Ratan, Minnesota Department of Agriculture, National Institute of Food and Agriculture (US), Department of Energy (US), Austrian Academy of Sciences, Max Planck Society, European Commission, European Research Council, and Federal Ministry of Education and Research (Germany)

Subjects
Comparative genomics, Genetic mapping, Molecular Sequence Annotation, Plant Science, Genome annotations, Genomeassembly, Chromosomes, Thlaspi, Translational Research, Biomedical, genome assembly, Pennycress, Agronomy and Crop Science, Ecosystem, Genome, Plant, Biotechnology
Abstract

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae., This material is based upon work that is supported by the Minnesota Department of Agriculture (J.A., K.F., R.C.) and by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award numbers 2018-67009-27374 (J.A., R.C., K.F.), and 2019-67009-29004 (M.D.M, J.S.) and the Agriculture and Food Research Initiative Competitive Grant No. 2019-69012-29851 (M.D.M, R.C., J.S.). This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Science Program grant no. DE-SC0021286 (M.D.M, R.C.). This work was further funded by the Austrian Academy of Sciences (C.B., I.R.A., K.J., D.R.C.); the Max Planck Society (D.W., A.C.G., P.C.B., C.L.); the European Union’s Horizon 2020 research and innovation programme by the European Research Council (ERC), Grant Agreement No. 716823 ‘FEAR-SAP’ (I.R.A., C.B.), by the Marie Sklodowska-Curie ETN ‘EpiDiverse’, Grant Agreement No. 764965 (D.R.C., C.B.) and by Marie Sklodowska-Curie, Grant Agreement MSCA-IF No 797460 (P.C.B.); and the German Federal Ministry of Education and Research BMBF, Grant No. 031A538A, de.NBI-RBC (A.N., P.F.S.).

Published
2021

43. Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Author

Kersten, Sonja, primary, Chang, Jiyang, additional, Huber, Christian D., additional, Voichek, Yoav, additional, Lanz, Christa, additional, Hagmaier, Timo, additional, Lang, Patricia, additional, Lutz, Ulrich, additional, Hirschberg, Insa, additional, Lerchl, Jens, additional, Porri, Aimone, additional, Van de Peer, Yves, additional, Schmid, Karl, additional, Weigel, Detlef, additional, and Rabanal, Fernando A., additional

Published
2021
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44. Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

Author

Todesco, Marco, Balasubramanian, Sureshkumar, Hu, Tina T., Traw, M. Brian, Horton, Matthew, Epple, Petra, Kuhns, Christine, Sureshkumar, Sridevi, Schwartz, Christopher, Lanz, Christa, Laitinen, Roosa A.E., Huang, Yu, Chory, Joanne, Lipka, Volker, Borevitz, Justin O., Dangl, Jeffery L., Bergelson, Joy, Nordborg, Magnus, and Weigel, Detlef

Subjects
Identification and classification, Research, Genetic aspects, Alleles -- Identification and classification -- Research -- Genetic aspects, Arabidopsis thaliana -- Genetic aspects -- Research, Genetic variation -- Identification and classification -- Genetic aspects -- Research, Fitness (Genetics) -- Research -- Genetic aspects, Allelomorphism -- Identification and classification -- Research -- Genetic aspects
Abstract

A survey of A. thaliana accessions collected from the wild revealed extensive environment-dependent variation for leaf initiation rate (Supplementary Table 1). One of the strains, Est-1, which produced leaves more [...], Plants can defend themselves against a wide array of enemies, from microbes to large animals, yet there is great variability in the effectiveness of such defences, both within and between species. Some of this variation can be explained by conflicting pressures from pathogens with different modes of attack (1). A second explanation comes from an evolutionary 'tug of war', in which pathogens adapt to evade detection, until the plant has evolved new recognition capabilities for pathogen invasion (2-5). If selection is, however, sufficiently strong, susceptible hosts should remain rare. That this is not the case is best explained by costs incurred from constitutive defences in a pest-free environment (6-11). Using a combination of forward genetics and genome-wide association analyses, we demonstrate that allelic diversity at a single locus, ACCELERATED CELL DEATH 6 (ACD6) (12,13), underpins marked pleiotropic differences in both vegetative growth and resistance to microbial infection and herbivory among natural Arabidopsis thaliana strains. A hyperactive ACD6 allele, compared to the reference allele, strongly enhances resistance to a broad range of pathogens from different phyla, but at the same time slows the production of new leaves and greatly reduces the biomass of mature leaves. This allele segregates at intermediate frequency both throughout the worldwide range of A. thaliana and within local populations, consistent with this allele providing substantial fitness benefits despite its marked impact on growth.

Published
2010
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45. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Author

Nunn, Adam, primary, Rodríguez-Arévalo, Isaac, additional, Tandukar, Zenith, additional, Frels, Katherine, additional, Contreras-Garrido, Adrián, additional, Carbonell-Bejerano, Pablo, additional, Zhang, Panpan, additional, Ramos-Cruz, Daniela, additional, Jandrasits, Katharina, additional, Lanz, Christa, additional, Brusa, Anthony, additional, Mirouze, Marie, additional, Dorn, Kevin, additional, Jarvis, Brice, additional, Sedbrook, John, additional, Wyse, Donald L., additional, Otto, Christian, additional, Langenberger, David, additional, Stadler, Peter F., additional, Weigel, Detlef, additional, Marks, M. David, additional, Anderson, James A., additional, Becker, Claude, additional, and Chopra, Ratan, additional

Published
2021
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46. Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

Author

Hanikenne, Marc, Talke, Ina N., Haydon, Michael J., Lanz, Christa, Nolte, Andrea, Motte, Patrick, Kroymann, Juergen, Weigel, Detlef, and Kramer, Ute

Subjects
Gene mutations -- Research -- Physiological aspects -- Genetic aspects, Arabidopsis -- Physiological aspects -- Genetic aspects -- Research, Animal mutation -- Physiological aspects -- Genetic aspects -- Research, Bioaccumulation -- Evaluation -- Genetic aspects -- Research -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Evaluation, Physiological aspects, Genetic aspects, Research
Abstract

Little is known about the types of mutations underlying the evolution of species-specific traits. The metal hyperaccumulator Arabidopsis halleri has the rare ability to colonize heavy-metal-polluted soils, and, as an [...]

Published
2008

47. Clonal improvement-associated somatic mutations identified from diploid genome assembly in Tempranillo grapevine cultivar

Author

Carbonell-Bejerano, Pablo, Bezrukov, Ilja, Alañón-Sánchez, Noelia, Royo, Carolina, Ferradas, Yolanda, Lanz, Christa, Ibáñez Marcos, Javier, Martínez-Zapater, José M., Weigel, Detlef, Carbonell-Bejerano, Pablo, Bezrukov, Ilja, Alañón-Sánchez, Noelia, Royo, Carolina, Ferradas, Yolanda, Lanz, Christa, Ibáñez Marcos, Javier, Martínez-Zapater, José M., and Weigel, Detlef

Abstract

Tempranillo is the third most widely grown red wine cultivar worldwide and the most relevant in the Iberian Peninsula. Here we produced a diploid genome assembly of Tempranillo to study the origin of clonal improvement in this cultivar. After PacBio and Oxford Nanopore sequencing, a trio binning approach produced chromosome-arm level and complete assemblies for the two haplo-phases. Based on the de novo assembly, we searched for genetic variation in ten re-sequenced Tempranillo clones selected for variation in agronomically relevant traits including fruit colour, low fruit sugar accumulation adaptable to warmer climates or loose bunches that are less prone to fungal diseases. Thousands of somatic mutations were detected in the ten clones, which, combined with gene annotations based on PacBio Iso-seq, identified candidate dominant missense variants related with selected phenotypes. We could also phase inter-chromosomal structural variation (SV) in the origin of white gape and loose cluster phenotypes. Our results provide a quality genome assembly for inter- and intra-cultivar comparisons and release candidate missense and SV mutations that could be responsible for clonal diversification and improvement.

Published
2021

48. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence

Author

Thieme, Frank, Koebnik, Ralf, Bekel, Thomas, Berger, Carolin, Boch, Jens, Buttner, Daniela, Caldana, Camila, Gaigalat, Lars, Goesmann, Alexander, Kay, Sabine, Kirchner, Oliver, Lanz, Christa, Linke, Burkhard, McHardy, Alice C., Meyer, Folker, Mittenhuber, Gerhard, Nies, Dietrich H., Niesbach-Klosgen, Ulla, Patschkowski, Thomas, Ruckert, Christian, Rupp, Oliver, Schneiker, Susanne, Schuster, Stephan C., Vorholter, Frank-Jorg, Weber, Ernst, Puhler, Alfred, Bonas, Ulla, Bartels, Daniela, and Kaiser, Olaf

Subjects
Nucleotide sequence -- Research, Microbial polysaccharides -- Research, Bacterial proteins -- Research, Genetic research, Biological sciences
Abstract

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity., the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.

Published
2005

49. A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus

Author

Srinivasan, Jagan, Sinz, Waltraud, Lanz, Christa, Brand, Alexandra, Nandakumar, Ramkumar, Raddatz, Gunter, Witte, Hanh, Keller, Heike, Kipping, Isabel, Pires-daSilva, Andre, Jesse, Taco, Millare, Jun, de Both, Michiel, Schuster, Stephan C., and Sommer, Ralf J.

Subjects
Genetics -- Research, Chromosome mapping -- Genetic aspects, Evolution -- Research, Evolution -- Genetic aspects, Roundworm -- Genetic aspects, Nematoda, Variation (Biology) -- Genetic aspects, Variation (Biology) -- Research, Genetic markers -- Research, Biological sciences
Abstract

To understand the evolution of developmental processes, nonmodel organisms in the nematodes, insects, and vertebrates are compared with established model systems. Often, these comparisons suffer from the inability to apply sophisticated technologies to these nonmodel species. In the nematode Pristionchus pacificus, cellular and genetic analyses are used to compare vulva development to that of Caenorhabditis elegans. However, substantial changes in gene function between P. pacificus and C. elegans limit the use of candidate gene approaches in studying P. pacificus mutations. To facilitate map-based cloning of mutations in P. pacificus, we constructed a BAC-based genetic linkage map. A BAC library of 13,440 clones was generated and completely end sequenced. By comparing BAC end and EST sequences between the 'wild-type' strain P. pacificus var. California and the polymorphic strain P. pacificus var. Washington, 133 single-stranded conformational polymorphisms were identified. These markers were tested on a meiotic mapping panel of 46 randomly picked [F.sub.2] animals after a cross of the two strains, providing' the first genetic linkage map of P. pacificus. A mapping strategy using two selected markers per chromosome was devised and the efficiency of this approach was illustrated by the mapping of the Ppa-unc-1/Twitchin gene.

Published
2002

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