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146 results on '"Witek, Kamil"'

1. On-line Anomaly Detection and Qualification of Random Bit Streams

Author

Caratozzolo, Cesare, Rossi, Valeria, Witek, Kamil, Trombetta, Alberto, and Caccia, Massimo

Subjects
Computer Science - Cryptography and Security
Abstract

Generating random bit streams is required in various applications, most notably cyber-security. Ensuring high-quality and robust randomness is crucial to mitigate risks associated with predictability and system compromise. True random numbers provide the highest unpredictability levels. However, potential biases in the processes exploited for the random number generation must be carefully monitored. This paper reports the implementation and characterization of an on-line procedure for the detection of anomalies in a true random bit stream. It is based on the NIST Adaptive Proportion and Repetition Count tests, complemented by statistical analysis relying on the Monobit and RUNS. The procedure is firmware implemented and performed simultaneously with the bit stream generation, and providing as well an estimate of the entropy of the source. The experimental validation of the approach is performed upon the bit streams generated by a quantum, silicon-based entropy source., Comment: 9 pages, 12 figures, 3 tables, submitted at IEEE CSR 2024

Published
2024

2. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors

Author

Lin, Xiao, Jia, Yuxin, Heal, Robert, Prokchorchik, Maxim, Sindalovskaya, Maria, Olave-Achury, Andrea, Makechemu, Moffat, Fairhead, Sebastian, Noureen, Azka, Heo, Jung, Witek, Kamil, Smoker, Matthew, Taylor, Jodie, Shrestha, Ram-Krishna, Lee, Yoonyoung, Zhang, Chunzhi, Park, Soon Ju, Sohn, Kee Hoon, Huang, Sanwen, and Jones, Jonathan D. G.

Published
2023
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3. Publisher Correction: Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors

Author

Lin, Xiao, Jia, Yuxin, Heal, Robert, Prokchorchik, Maxim, Sindalovskaya, Maria, Olave-Achury, Andrea, Makechemu, Moffat, Fairhead, Sebastian, Noureen, Azka, Heo, Jung, Witek, Kamil, Smoker, Matthew, Taylor, Jodie, Shrestha, Ram-Krishna, Lee, Yoonyoung, Zhang, Chunzhi, Park, Soon Ju, Sohn, Kee Hoon, Huang, Sanwen, and Jones, Jonathan D. G.

Published
2023
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6. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector

Author

Witek, Kamil, Lin, Xiao, Karki, Hari S., Jupe, Florian, Witek, Agnieszka I., Steuernagel, Burkhard, Stam, Remco, van Oosterhout, Cock, Fairhead, Sebastian, Heal, Robert, Cocker, Jonathan M., Bhanvadia, Shivani, Barrett, William, Wu, Chih-Hang, Adachi, Hiroaki, Song, Tianqiao, Kamoun, Sophien, Vleeshouwers, Vivianne G. A. A., Tomlinson, Laurence, Wulff, Brande B. H., and Jones, Jonathan D. G.

Published
2021
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10. Rapid Discovery of Functional NLRs Using the Signature of High Expression, High-Throughput Transformation, and Large-Scale Phenotyping

Author

Brabham, Helen Jane, primary, Hernández-Pinzón, Inmaculada, additional, Yanagihara, Chizu, additional, Ishikawa, Noriko, additional, Komori, Toshiyuki, additional, Matny, Oadi N., additional, Hubbard, Amelia, additional, Witek, Kamil, additional, Numazawa, Hironobu, additional, Green, Phon, additional, Dreiseitl, Antonín, additional, Takemori, Naoki, additional, Komari, Toshihiko, additional, Freedman, Roger P., additional, Steffenson, Brian, additional, van Esse, H. Peter, additional, and Moscou, Matthew James, additional

Published
2023
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14. The Solanum americanum pangenome and effectoromics reveal new resistance genes against potato late blight

Author

Lin, Xiao, primary, Jia, Yuxin, additional, Heal, Robert, additional, Prokchorchik, Maxim, additional, Sindalovskaya, Maria, additional, Olave-Achury, Andrea, additional, Makechemu, Moffat, additional, Fairhead, Sebastian, additional, Noureen, Azka, additional, Heo, Jung, additional, Witek, Kamil, additional, Smoker, Matthew, additional, Taylor, Jodie, additional, Shrestha, Ram-Krishna, additional, Lee, Yoonyoung, additional, Zhang, Chunzhi, additional, Park, Soon Ju, additional, Sohn, Kee Hoon, additional, Huang, Sanwen, additional, and Jones, Jonathan D. G., additional

Published
2022
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17. Identification of RipAZ1 as an avirulence determinant of Ralstonia solanacearum in Solanum americanum

Author

Moon, Hayoung, Pandey, Ankita, Yoon, Hayeon, Choi, Sera, Jeon, Hyelim, Prokchorchik, Maxim, Jung, Gayoung, Witek, Kamil, Valls, Marc, McCann, Honour C., Kim, Min-Sung, Jones, Jonathan D. G., Segonzac, Cécile, Sohn, Kee Hoon, Moon, Hayoung, Pandey, Ankita, Yoon, Hayeon, Choi, Sera, Jeon, Hyelim, Prokchorchik, Maxim, Jung, Gayoung, Witek, Kamil, Valls, Marc, McCann, Honour C., Kim, Min-Sung, Jones, Jonathan D. G., Segonzac, Cécile, and Sohn, Kee Hoon

Abstract

Altres ajuts: CERCA Programme/Generalitat de Catalunya, Ralstonia solanacearum causes bacterial wilt disease in many plant species. Type III-secreted effectors (T3Es) play crucial roles in bacterial pathogenesis. However, some T3Es are recognized by corresponding disease resistance proteins and activate plant immunity. In this study, we identified the R. solanacearum T3E protein RipAZ1 (Ralstonia injected protein AZ1) as an avirulence determinant in the black nightshade species Solanum americanum. Based on the S. americanum accession-specific avirulence phenotype of R. solanacearum strain Pe_26, 12 candidate avirulence T3Es were selected for further analysis. Among these candidates, only RipAZ1 induced a cell death response when transiently expressed in a bacterial wilt-resistant S. americanum accession. Furthermore, loss of ripAZ1 in the avirulent R. solanacearum strain Pe_26 resulted in acquired virulence. Our analysis of the natural sequence and functional variation of RipAZ1 demonstrated that the naturally occurring C-terminal truncation results in loss of RipAZ1-triggered cell death. We also show that the 213 amino acid central region of RipAZ1 is sufficient to induce cell death in S. americanum. Finally, we show that RipAZ1 may activate defence in host cell cytoplasm. Taken together, our data indicate that the nucleocytoplasmic T3E RipAZ1 confers R. solanacearum avirulence in S. americanum. Few avirulence genes are known in vascular bacterial phytopathogens and ripAZ1 is the first one in R. solanacearum that is recognized in black nightshades. This work thus opens the way for the identification of disease resistance genes responsible for the specific recognition of RipAZ1, which can be a source of resistance against the devastating bacterial wilt disease. Ralstonia solanacearum type III effector RipAZ1 confers bacterial avirulence during interaction with a wild plant species Solanum americanum.

Published
2021

18. Identification of RipAZ1 as an avirulence determinant of Ralstonia solanacearum in Solanum americanum

Author

National Research Foundation of Korea, Rural Development Administration (South Korea), Government of South Korea, Seoul National University, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Moon, Hayoung, Pandey, Ankita, Yoon, Hayeon, Choi, Sera, Jeon, Hyelim, Prokchorchik, Maxim, Jung, Gayoung, Witek, Kamil, Valls, Marc, McCann, Honour C., Kim, Min-Sung, Jones, Jonathan D. G., Segonzac, Cécile, Sohn, Kee Hoon, National Research Foundation of Korea, Rural Development Administration (South Korea), Government of South Korea, Seoul National University, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Moon, Hayoung, Pandey, Ankita, Yoon, Hayeon, Choi, Sera, Jeon, Hyelim, Prokchorchik, Maxim, Jung, Gayoung, Witek, Kamil, Valls, Marc, McCann, Honour C., Kim, Min-Sung, Jones, Jonathan D. G., Segonzac, Cécile, and Sohn, Kee Hoon

Abstract

Ralstonia solanacearum causes bacterial wilt disease in many plant species. Type III-secreted effectors (T3Es) play crucial roles in bacterial pathogenesis. However, some T3Es are recognized by corresponding disease resistance proteins and activate plant immunity. In this study, we identified the R. solanacearum T3E protein RipAZ1 (Ralstonia injected protein AZ1) as an avirulence determinant in the black nightshade species Solanum americanum. Based on the S. americanum accession-specific avirulence phenotype of R. solanacearum strain Pe_26, 12 candidate avirulence T3Es were selected for further analysis. Among these candidates, only RipAZ1 induced a cell death response when transiently expressed in a bacterial wilt-resistant S. americanum accession. Furthermore, loss of ripAZ1 in the avirulent R. solanacearum strain Pe_26 resulted in acquired virulence. Our analysis of the natural sequence and functional variation of RipAZ1 demonstrated that the naturally occurring C-terminal truncation results in loss of RipAZ1-triggered cell death. We also show that the 213 amino acid central region of RipAZ1 is sufficient to induce cell death in S. americanum. Finally, we show that RipAZ1 may activate defence in host cell cytoplasm. Taken together, our data indicate that the nucleocytoplasmic T3E RipAZ1 confers R. solanacearum avirulence in S. americanum. Few avirulence genes are known in vascular bacterial phytopathogens and ripAZ1 is the first one in R. solanacearum that is recognized in black nightshades. This work thus opens the way for the identification of disease resistance genes responsible for the specific recognition of RipAZ1, which can be a source of resistance against the devastating bacterial wilt disease.

Published
2021

19. Solanum americanumgenome-assisted discovery of immune receptors that detect potato late blight pathogen effectors

Author

Lin, Xiao, Jia, Yuxin, Heal, Robert, Prokchorchik, Maxim, Sindalovskaya, Maria, Olave-Achury, Andrea, Makechemu, Moffat, Fairhead, Sebastian, Noureen, Azka, Heo, Jung, Witek, Kamil, Smoker, Matthew, Taylor, Jodie, Shrestha, Ram-Krishna, Lee, Yoonyoung, Zhang, Chunzhi, Park, Soon Ju, Sohn, Kee Hoon, Huang, Sanwen, and Jones, Jonathan D. G.

Abstract

Potato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanumaccessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanumimmune receptor genes. We further screened for variation in recognition of 315P. infestansRXLR effectors in 52 S. americanumaccessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860and R04373, that recognize cognate P. infestansRXLR effectors PITG_22825(AVRamr4), PITG_02860and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.

Published
2023
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22. The Rysto immune receptor recognises a broadly conserved feature of potyviral coat proteins.

Author

Grech‐Baran, Marta, Witek, Kamil, Poznański, Jarosław T., Grupa‐Urbańska, Anna, Malinowski, Tadeusz, Lichocka, Małgorzata, Jones, Jonathan D. G., and Hennig, Jacek

Subjects
*POTATO virus Y, *TURNIP mosaic virus, *COAT proteins (Viruses), *DISEASE resistance of plants, *AMINO acid residues, *POXVIRUSES
Abstract

Summary: Knowledge of the immune mechanisms responsible for viral recognition is critical for understanding durable disease resistance and successful crop protection. We determined how potato virus Y (PVY) coat protein (CP) is recognised by Rysto, a TNL immune receptor.We applied structural modelling, site‐directed mutagenesis, transient overexpression, co‐immunoprecipitation, infection assays and physiological cell death marker measurements to investigate the mechanism of Rysto–CP interaction.Rysto associates directly with PVY CP in planta that is conditioned by the presence of a CP central 149 amino acids domain. Each deletion that affects the CP core region impairs the ability of Rysto to trigger defence. Point mutations in the amino acid residues Ser125, Arg157, and Asp201 of the conserved RNA‐binding pocket of potyviral CP reduce or abolish Rysto binding and Rysto‐dependent responses, demonstrating that appropriate folding of the CP core is crucial for Rysto‐mediated recognition.Rysto recognises the CPs of at least 10 crop‐damaging viruses that share a similar core region. It confers immunity to plum pox virus and turnip mosaic virus in both Solanaceae and Brassicaceae systems, demonstrating potential utility in engineering virus resistance in various crops. Our findings shed new light on how R proteins detect different viruses by sensing conserved structural patterns. [ABSTRACT FROM AUTHOR]

Published
2022
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23. The NLR-annotator tool enables annotation of the intracellular immune receptor repertoire

Author

Steuernagel, Burkhard, Witek, Kamil, Krattinger, Simon G, Ramirez-Gonzalez, Ricardo H, Schoonbeek, Henk-jan, Yu, Guotai, Baggs, Erin, Witek, Agnieszka I, Yadav, Inderjit, Krasileva, Ksenia V, Jones, Jonathan D G, Uauy, Cristobal, Keller, Beat, Ridout, Christopher J, Wulff, Brande B H, University of Zurich, and Wulff, Brande B H

Subjects
10126 Department of Plant and Microbial Biology, 1311 Genetics, Physiology, 1110 Plant Science, Genetics, 1314 Physiology, Plant Science, 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center
Published
2020

24. Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq)

Author

Lin, Xiao, Song, Tianqiao, Fairhead, Sebastian, Witek, Kamil, Jouet, Agathe, Jupe, Florian, Witek, Agnieszka I., Karki, Hari S., Vleeshouwers, Vivianne G.A.A., Hein, Ingo, Jones, Jonathan D.G., Lin, Xiao, Song, Tianqiao, Fairhead, Sebastian, Witek, Kamil, Jouet, Agathe, Jupe, Florian, Witek, Agnieszka I., Karki, Hari S., Vleeshouwers, Vivianne G.A.A., Hein, Ingo, and Jones, Jonathan D.G.

Abstract

Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.

Published
2020

25. The NLR-annotator tool enables annotation of the intracellular immune receptor repertoire

Author

Steuernagel, Burkhard; https://orcid.org/0000-0002-8284-7728, Witek, Kamil; https://orcid.org/0000-0003-0659-5562, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Ramirez-Gonzalez, Ricardo H; https://orcid.org/0000-0001-5745-7085, Schoonbeek, Henk-jan; https://orcid.org/0000-0002-1087-2553, Yu, Guotai, Baggs, Erin; https://orcid.org/0000-0003-3076-9489, Witek, Agnieszka I; https://orcid.org/0000-0001-7395-687X, Yadav, Inderjit, Krasileva, Ksenia V; https://orcid.org/0000-0002-1679-0700, Jones, Jonathan D G; https://orcid.org/0000-0002-4953-261X, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Ridout, Christopher J; https://orcid.org/0000-0001-9287-938X, Wulff, Brande B H; https://orcid.org/0000-0003-4044-4346, Steuernagel, Burkhard; https://orcid.org/0000-0002-8284-7728, Witek, Kamil; https://orcid.org/0000-0003-0659-5562, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Ramirez-Gonzalez, Ricardo H; https://orcid.org/0000-0001-5745-7085, Schoonbeek, Henk-jan; https://orcid.org/0000-0002-1087-2553, Yu, Guotai, Baggs, Erin; https://orcid.org/0000-0003-3076-9489, Witek, Agnieszka I; https://orcid.org/0000-0001-7395-687X, Yadav, Inderjit, Krasileva, Ksenia V; https://orcid.org/0000-0002-1679-0700, Jones, Jonathan D G; https://orcid.org/0000-0002-4953-261X, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Ridout, Christopher J; https://orcid.org/0000-0001-9287-938X, and Wulff, Brande B H; https://orcid.org/0000-0003-4044-4346

Abstract

Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny, and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress, we found up-regulation of 266 of the NLRs To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.

Published
2020

26. Identification of RipAZ1 as an avirulence determinant ofRalstonia solanacearuminSolanum americanum

Author

Moon, Hayoung, primary, Pandey, Ankita, additional, Yoon, Hayeon, additional, Choi, Sera, additional, Jeon, Hyelim, additional, Prokchorchik, Maxim, additional, Jung, Gayoung, additional, Witek, Kamil, additional, Valls, Marc, additional, McCann, Honour C., additional, Kim, Min‐Sung, additional, Jones, Jonathan D. G., additional, Segonzac, Cécile, additional, and Sohn, Kee Hoon, additional

Published
2021
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28. Identification ofAvramr1fromPhytophthora infestansusing long read and cDNA pathogen‐enrichment sequencing (PenSeq)

Author

Lin, Xiao, primary, Song, Tianqiao, additional, Fairhead, Sebastian, additional, Witek, Kamil, additional, Jouet, Agathe, additional, Jupe, Florian, additional, Witek, Agnieszka I., additional, Karki, Hari S., additional, Vleeshouwers, Vivianne G. A. A., additional, Hein, Ingo, additional, and Jones, Jonathan D. G., additional

Published
2020
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29. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector

Author

Witek, Kamil, primary, Lin, Xiao, additional, Karki, Hari S, additional, Jupe, Florian, additional, Witek, Agnieszka I, additional, Steuernagel, Burkhard, additional, Stam, Remco, additional, van Oosterhout, Cock, additional, Fairhead, Sebastian, additional, Cocker, Jonathan M, additional, Bhanvadia, Shivani, additional, Barrett, William, additional, Wu, Chih-Hang, additional, Adachi, Hiroaki, additional, Song, Tianqiao, additional, Kamoun, Sophien, additional, Vleeshouwers, Vivianne GAA, additional, Tomlinson, Laurence, additional, Wulff, Brande BH, additional, and Jones, Jonathan DG, additional

Published
2020
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30. The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire

Author

Steuernagel, Burkhard, primary, Witek, Kamil, additional, Krattinger, Simon G., additional, Ramirez-Gonzalez, Ricardo H., additional, Schoonbeek, Henk-jan, additional, Yu, Guotai, additional, Baggs, Erin, additional, Witek, Agnieszka I., additional, Yadav, Inderjit, additional, Krasileva, Ksenia V., additional, Jones, Jonathan D.G., additional, Uauy, Cristobal, additional, Keller, Beat, additional, Ridout, Christopher J., additional, and Wulff, Brande B.H., additional

Published
2020
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32. A species-wide inventory of NLR genes and alleles in Arabidopsis thaliana

Author

Gordon and Betty Moore Foundation, Two Blades Foundation, Gatsby Charitable Foundation, Biotechnology and Biological Sciences Research Council (UK), National Science Foundation (US), European Research Council, Max Planck Society, Weyer, Anna-Lena van de, Monteiro, Freddy, Furzer, Oliver J., Nishimura, Marc T., Cevik, Volkan, Witek, Kamil, Jones, Jonathan D. G., Dangl, Jeffery L., Weigel, Detlef, Bemm, Felix, Gordon and Betty Moore Foundation, Two Blades Foundation, Gatsby Charitable Foundation, Biotechnology and Biological Sciences Research Council (UK), National Science Foundation (US), European Research Council, Max Planck Society, Weyer, Anna-Lena van de, Monteiro, Freddy, Furzer, Oliver J., Nishimura, Marc T., Cevik, Volkan, Witek, Kamil, Jones, Jonathan D. G., Dangl, Jeffery L., Weigel, Detlef, and Bemm, Felix

Abstract

Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes.

Published
2019

35. Additional file 3: of Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

Author

Pais, Marina, Yoshida, Kentaro, Giannakopoulou, Artemis, Pel, Mathieu, Cano, Liliana, Oliva, Ricardo, Witek, Kamil, Lindqvist-Kreuze, Hannele, Vleeshouwers, Vivianne, and Sophien Kamoun

Subjects
fungi
Abstract

One-tailed hypergeometric tests performed for enrichment analyses to assess effector bias and GSR bias in the sets of polymorphic genes. (PDF 242 kb)

Published
2018
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37. TheArabidopsis thalianapan-NLRome

Author

Van de Weyer, Anna-Lena, primary, Monteiro, Freddy, additional, Furzer, Oliver J., additional, Nishimura, Marc T., additional, Cevik, Volkan, additional, Witek, Kamil, additional, Jones, Jonathan D.G., additional, Dangl, Jeffery L., additional, Weigel, Detlef, additional, and Bemm, Felix, additional

Published
2019
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38. Shifting the limits in wheat research and breeding using a fully annotated reference genome

Author

Appels, Rudi, Eversole, Kellye, Stein, Nils, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Sharpe, Andrew G., Barad, Omer, Baruch, Kobi, Keeble-gagnère, Gabriel, Mascher, Martin, Ben-zvi, Gil, Josselin, Ambre-aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-gonzalez, Juan, Hayden, Matthew, Koh, Chushin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel, Lang, Daniel, Gundlach, Heidrun, Haberer, Georg, Mayer, Klaus F. X., Ormanbekova, Danara, Prade, Verena, Šimková, Hana, Wicker, Thomas, Swarbreck, David, Rimbert, Hélène, Felder, Marius, Guilhot, Nicolas, Kaithakottil, Gemy, Keilwagen, Jens, Leroy, Philippe, Lux, Thomas, Twardziok, Sven, Venturini, Luca, Juhász, Angéla, Abrouk, Michael, Fischer, Iris, Uauy, Cristobal, Borrill, Philippa, Ramirez-gonzalez, Ricardo H., Arnaud, Dominique, Chalabi, Smahane, Chalhoub, Boulos, Cory, Aron, Datla, Raju, Davey, Mark W., Jacobs, John, Robinson, Stephen J., Steuernagel, Burkhard, Van Ex, Fred, Wulff, Brande B. H., Benhamed, Moussa, Bendahmane, Abdelhafid, Concia, Lorenzo, Latrasse, David, Bartoš, Jan, Bellec, Arnaud, Berges, Hélène, Doležel, Jaroslav, Frenkel, Zeev, Gill, Bikram, Korol, Abraham, Letellier, Thomas, Olsen, Odd-arne, Singh, Kuldeep, Valárik, Miroslav, Van Der Vossen, Edwin, Vautrin, Sonia, Weining, Song, Fahima, Tzion, Glikson, Vladimir, Raats, Dina, Číhalíková, Jarmila, Toegelová, Helena, Vrána, Jan, Sourdille, Pierre, Darrier, Benoit, Barabaschi, Delfina, Cattivelli, Luigi, Hernandez, Pilar, Galvez, Sergio, Budak, Hikmet, Jones, Jonathan D. G., Witek, Kamil, Yu, Guotai, Small, Ian, Melonek, Joanna, Zhou, Ruonan, Belova, Tatiana, Kanyuka, Kostya, King, Robert, Nilsen, Kirby, Walkowiak, Sean, Cuthbert, Richard, Knox, Ron, Wiebe, Krysta, Xiang, Daoquan, Rohde, Antje, Golds, Timothy, Čížková, Jana, Akpinar, Bala Ani, Biyiklioglu, Sezgi, Gao, Liangliang, N’daiye, Amidou, Kubaláková, Marie, Šafář, Jan, Alfama, Françoise, Adam-blondon, Anne-françoise, Flores, Raphael, Guerche, Claire, Loaec, Mikaël, Quesneville, Hadi, Condie, Janet, Ens, Jennifer, Maclachlan, Ron, Tan, Yifang, Alberti, Adriana, Aury, Jean-marc, Barbe, Valérie, Couloux, Arnaud, Cruaud, Corinne, Labadie, Karine, Mangenot, Sophie, Wincker, Patrick, Kaur, Gaganpreet, Luo, Mingcheng, Sehgal, Sunish, Chhuneja, Parveen, Gupta, Om Prakash, Jindal, Suruchi, Kaur, Parampreet, Malik, Palvi, Sharma, Priti, Yadav, Bharat, Singh, Nagendra K., Khurana, Jitendra P., Chaudhary, Chanderkant, Khurana, Paramjit, Kumar, Vinod, Mahato, Ajay, Mathur, Saloni, Sevanthi, Amitha, Sharma, Naveen, Tomar, Ram Sewak, Holušová, Kateřina, Plíhal, Ondřej, Clark, Matthew D., Heavens, Darren, Kettleborough, George, Wright, Jon, Balcárková, Barbora, Hu, Yuqin, Salina, Elena, Ravin, Nikolai, Skryabin, Konstantin, Beletsky, Alexey, Kadnikov, Vitaly, Mardanov, Andrey, Nesterov, Michail, Rakitin, Andrey, Sergeeva, Ekaterina, Handa, Hirokazu, Kanamori, Hiroyuki, Katagiri, Satoshi, Kobayashi, Fuminori, Nasuda, Shuhei, Tanaka, Tsuyoshi, Wu, Jianzhong, Cattonaro, Federica, Jiumeng, Min, Kugler, Karl, Pfeifer, Matthias, Sandve, Simen, Xun, Xu, Zhan, Bujie, Batley, Jacqueline, Bayer, Philipp E., Edwards, David, Hayashi, Satomi, Tulpová, Zuzana, Visendi, Paul, Cui, Licao, Du, Xianghong, Feng, Kewei, Nie, Xiaojun, Tong, Wei, Wang, Le, Appels, Rudi, Eversole, Kellye, Stein, Nils, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Sharpe, Andrew G., Barad, Omer, Baruch, Kobi, Keeble-gagnère, Gabriel, Mascher, Martin, Ben-zvi, Gil, Josselin, Ambre-aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-gonzalez, Juan, Hayden, Matthew, Koh, Chushin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel, Lang, Daniel, Gundlach, Heidrun, Haberer, Georg, Mayer, Klaus F. X., Ormanbekova, Danara, Prade, Verena, Šimková, Hana, Wicker, Thomas, Swarbreck, David, Rimbert, Hélène, Felder, Marius, Guilhot, Nicolas, Kaithakottil, Gemy, Keilwagen, Jens, Leroy, Philippe, Lux, Thomas, Twardziok, Sven, Venturini, Luca, Juhász, Angéla, Abrouk, Michael, Fischer, Iris, Uauy, Cristobal, Borrill, Philippa, Ramirez-gonzalez, Ricardo H., Arnaud, Dominique, Chalabi, Smahane, Chalhoub, Boulos, Cory, Aron, Datla, Raju, Davey, Mark W., Jacobs, John, Robinson, Stephen J., Steuernagel, Burkhard, Van Ex, Fred, Wulff, Brande B. H., Benhamed, Moussa, Bendahmane, Abdelhafid, Concia, Lorenzo, Latrasse, David, Bartoš, Jan, Bellec, Arnaud, Berges, Hélène, Doležel, Jaroslav, Frenkel, Zeev, Gill, Bikram, Korol, Abraham, Letellier, Thomas, Olsen, Odd-arne, Singh, Kuldeep, Valárik, Miroslav, Van Der Vossen, Edwin, Vautrin, Sonia, Weining, Song, Fahima, Tzion, Glikson, Vladimir, Raats, Dina, Číhalíková, Jarmila, Toegelová, Helena, Vrána, Jan, Sourdille, Pierre, Darrier, Benoit, Barabaschi, Delfina, Cattivelli, Luigi, Hernandez, Pilar, Galvez, Sergio, Budak, Hikmet, Jones, Jonathan D. G., Witek, Kamil, Yu, Guotai, Small, Ian, Melonek, Joanna, Zhou, Ruonan, Belova, Tatiana, Kanyuka, Kostya, King, Robert, Nilsen, Kirby, Walkowiak, Sean, Cuthbert, Richard, Knox, Ron, Wiebe, Krysta, Xiang, Daoquan, Rohde, Antje, Golds, Timothy, Čížková, Jana, Akpinar, Bala Ani, Biyiklioglu, Sezgi, Gao, Liangliang, N’daiye, Amidou, Kubaláková, Marie, Šafář, Jan, Alfama, Françoise, Adam-blondon, Anne-françoise, Flores, Raphael, Guerche, Claire, Loaec, Mikaël, Quesneville, Hadi, Condie, Janet, Ens, Jennifer, Maclachlan, Ron, Tan, Yifang, Alberti, Adriana, Aury, Jean-marc, Barbe, Valérie, Couloux, Arnaud, Cruaud, Corinne, Labadie, Karine, Mangenot, Sophie, Wincker, Patrick, Kaur, Gaganpreet, Luo, Mingcheng, Sehgal, Sunish, Chhuneja, Parveen, Gupta, Om Prakash, Jindal, Suruchi, Kaur, Parampreet, Malik, Palvi, Sharma, Priti, Yadav, Bharat, Singh, Nagendra K., Khurana, Jitendra P., Chaudhary, Chanderkant, Khurana, Paramjit, Kumar, Vinod, Mahato, Ajay, Mathur, Saloni, Sevanthi, Amitha, Sharma, Naveen, Tomar, Ram Sewak, Holušová, Kateřina, Plíhal, Ondřej, Clark, Matthew D., Heavens, Darren, Kettleborough, George, Wright, Jon, Balcárková, Barbora, Hu, Yuqin, Salina, Elena, Ravin, Nikolai, Skryabin, Konstantin, Beletsky, Alexey, Kadnikov, Vitaly, Mardanov, Andrey, Nesterov, Michail, Rakitin, Andrey, Sergeeva, Ekaterina, Handa, Hirokazu, Kanamori, Hiroyuki, Katagiri, Satoshi, Kobayashi, Fuminori, Nasuda, Shuhei, Tanaka, Tsuyoshi, Wu, Jianzhong, Cattonaro, Federica, Jiumeng, Min, Kugler, Karl, Pfeifer, Matthias, Sandve, Simen, Xun, Xu, Zhan, Bujie, Batley, Jacqueline, Bayer, Philipp E., Edwards, David, Hayashi, Satomi, Tulpová, Zuzana, Visendi, Paul, Cui, Licao, Du, Xianghong, Feng, Kewei, Nie, Xiaojun, Tong, Wei, and Wang, Le

Abstract

Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.

Published
2018

39. Extreme resistance to Potato virus Y in potato carrying the Rysto gene is mediated by a TIR‐NLR immune receptor.

Author

Grech‐Baran, Marta, Witek, Kamil, Szajko, Katarzyna, Witek, Agnieszka I., Morgiewicz, Karolina, Wasilewicz‐Flis, Iwona, Jakuczun, Henryka, Marczewski, Waldemar, Jones, Jonathan D. G., and Hennig, Jacek

Subjects
*POTATO virus Y, *TRANSGENIC plants, *POTATOES, *CROP losses, *VIRAL transmission
Abstract

Summary: Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Rysto, from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Rysto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Rysto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single‐molecule real‐time sequencing). Rysto was found to encode a nucleotide‐binding leucine‐rich repeat (NLR) protein with an N‐terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Rysto‐dependent extreme resistance was temperature‐independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY‐resistant cultivars of potato and other Solanaceae crops. [ABSTRACT FROM AUTHOR]

Published
2020
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41. SMRT RenSeq protocol

Author

Witek, Kamil, primary, Witek, Kamil, additional, Jupe, Florian, additional, Witek, Agnieszka I, additional, Baker, David, additional, Clark, Matthew D, additional, and Jones, Jonathan DG, additional

Published
2016
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44. Targeted capture and sequencing of gene-sized DNA molecules

Author

Giolai, Michael, primary, Paajanen, Pirita, additional, Verweij, Walter, additional, Percival-Alwyn, Lawrence, additional, Baker, David, additional, Witek, Kamil, additional, Jupe, Florian, additional, Bryan, Glenn, additional, Hein, Ingo, additional, Jones, Jonathan D. G., additional, and Clark, Matthew D., additional

Published
2016
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45. Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture

Author

Steuernagel, Burkhard, primary, Periyannan, Sambasivam K, additional, Hernández-Pinzón, Inmaculada, additional, Witek, Kamil, additional, Rouse, Matthew N, additional, Yu, Guotai, additional, Hatta, Asyraf, additional, Ayliffe, Mick, additional, Bariana, Harbans, additional, Jones, Jonathan D G, additional, Lagudah, Evans S, additional, and Wulff, Brande B H, additional

Published
2016
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47. Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species <italic>Solanum verrucosum</italic> through DNA capture technologies.

Author

Chen, Xinwei, Lewandowska, Dominika, Armstrong, Miles R., Baker, Katie, Lim, Tze-Yin, Bayer, Micha, Harrower, Brian, McLean, Karen, Jupe, Florian, Witek, Kamil, Lees, Alison K., Jones, Jonathan D., Bryan, Glenn J., and Hein, Ingo

Subjects
VEGETATION mapping, DIPLOIDY, CULTIVARS, POTATOES, PLANT species diversity, PLANT genetics, PLANT chromosomes
Abstract

Key message: A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes.Abstract: We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis. Both approaches independently positioned the resistance, referred to as Rpi-ver1, to the distal end of potato chromosome 9. Stringent post-enrichment read filtering identified a total of 64 informative SNPs that corresponded to the expected ratio for significant polymorphisms in the parents as well as the bulks. Of these, 61 SNPs are located on potato chromosome 9 and reside within 27 individual genes, which in the sequenced potato clone DM locate to positions 45.9 to 60.9 Mb. RenSeq- and GenSeq-derived SNPs within the target region were converted into allele-specific PCR-based KASP markers and further defined the position of the resistance to a 4.3 Mb interval at the bottom end of chromosome 9 between positions 52.62-56.98 Mb. [ABSTRACT FROM AUTHOR]

Published
2018
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48. Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea

Author

Trantas, Emmanouil A., primary, Licciardello, Grazia, additional, Almeida, Nalvo F., additional, Witek, Kamil, additional, Strano, Cinzia P., additional, Duxbury, Zane, additional, Ververidis, Filippos, additional, Goumas, Dimitrios E., additional, Jones, Jonathan D. G., additional, Guttman, David S., additional, Catara, Vittoria, additional, and Sarris, Panagiotis F., additional

Published
2015
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