22 results on '"Poretti, Manuel"'
Search Results
2. Biased Retention of Environment-Responsive Genes Following Genome Fractionation.
- Author
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Beringer, Marc, Choudhury, Rimjhim Roy, Mandáková, Terezie, Grünig, Sandra, Poretti, Manuel, Leitch, Ilia J, Lysak, Martin A, and Parisod, Christian
- Subjects
GENE expression ,GENES ,GENOMES ,BRASSICACEAE ,MUSTARD - Abstract
The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata ; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew
- Author
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Müller, Marion C., Praz, Coraline R., Sotiropoulos, Alexandros G., Menardo, Fabrizio, Kunz, Lukas, Schudel, Seraina, Oberhänsli, Simone, Poretti, Manuel, Wehrli, Andreas, Bourras, Salim, Keller, Beat, and Wicker, Thomas
- Published
- 2019
4. A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat
- Author
-
Kolodziej, Markus C., Singla, Jyoti, Sánchez-Martín, Javier, Zbinden, Helen, Šimková, Hana, Karafiátová, Miroslava, Doležel, Jaroslav, Gronnier, Julien, Poretti, Manuel, Glauser, Gaétan, Zhu, Wangsheng, Köster, Philipp, Zipfel, Cyril, Wicker, Thomas, Krattinger, Simon G., and Keller, Beat
- Published
- 2021
- Full Text
- View/download PDF
5. A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material
- Author
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Swiss National Science Foundation, University of Zurich, Poretti, Manuel [0000-0001-6915-2238], Praz, Coraline R. [0000-0002-9133-4406], Sotiropoulos, Alexandros G. [0000-0002-3591-0851], Wicker, Thomas [0000-0002-6777-7135], Poretti, Manuel, Praz, Coraline R., Sotiropoulos, Alexandros G., Wicker, Thomas, Swiss National Science Foundation, University of Zurich, Poretti, Manuel [0000-0001-6915-2238], Praz, Coraline R. [0000-0002-9133-4406], Sotiropoulos, Alexandros G. [0000-0002-3591-0851], Wicker, Thomas [0000-0002-6777-7135], Poretti, Manuel, Praz, Coraline R., Sotiropoulos, Alexandros G., and Wicker, Thomas
- Abstract
Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.
- Published
- 2023
6. A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material
- Author
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Poretti, Manuel, Praz, Coraline R, Sotiropoulos, Alexandros G, Wicker, Thomas, University of Zurich, Wicker, Thomas, Swiss National Science Foundation, Poretti, Manuel, Praz, Coraline R., and Sotiropoulos, Alexandros G.
- Subjects
Ecology ,Plant Science ,580 Plants (Botany) ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,1301 Biochemistry, Genetics and Molecular Biology (miscellaneous) ,UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,1105 Ecology, Evolution, Behavior and Systematics ,10126 Department of Plant and Microbial Biology ,1110 Plant Science ,Triticeae‐specific genes ,De novo gene evolution ,10211 Zurich-Basel Plant Science Center ,Stress adaptation ,Transposable elements ,2303 Ecology ,Ecology, Evolution, Behavior and Systematics - Abstract
16 Pág., Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins., This work was supported by the Swiss National Foundation grant 31003A_163325.University of Zurich Research Priority Program, Grant/Award Number: U-702-21-01; Swiss National Foundation, Grant/Award Number: 31003A_163325
- Published
- 2023
7. A survey of lineage‐specific genes in Triticeae reveals de novo gene evolution from genomic raw material
- Author
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Poretti, Manuel, primary, Praz, Coraline R., additional, Sotiropoulos, Alexandros G., additional, and Wicker, Thomas, additional
- Published
- 2023
- Full Text
- View/download PDF
8. A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material
- Author
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Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Praz, Coraline R; https://orcid.org/0000-0002-9133-4406, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Praz, Coraline R; https://orcid.org/0000-0002-9133-4406, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, and Wicker, Thomas; https://orcid.org/0000-0002-6777-7135
- Abstract
Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.
- Published
- 2023
9. Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons
- Author
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Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Stritt, Christoph; https://orcid.org/0000-0002-3167-6658, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Pozniak, Curtis J; https://orcid.org/0000-0002-7536-3856, Walkowiak, Sean, Gundlach, Heidrun; https://orcid.org/0000-0002-6757-0943, Stein, Nils; https://orcid.org/0000-0003-3011-8731, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Stritt, Christoph; https://orcid.org/0000-0002-3167-6658, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Pozniak, Curtis J; https://orcid.org/0000-0002-7536-3856, Walkowiak, Sean, Gundlach, Heidrun; https://orcid.org/0000-0002-6757-0943, and Stein, Nils; https://orcid.org/0000-0003-3011-8731
- Abstract
Wheat has one of the largest and most repetitive genomes among major crop plants, containing over 85% transposable elements (TEs). TEs populate genomes much in the way that individuals populate ecosystems, diversifying into different lineages, sub-families and sub-populations. The recent availability of high-quality, chromosome-scale genome sequences from ten wheat lines enables a detailed analysis how TEs evolved in allohexaploid wheat, its diploids progenitors, and in various chromosomal haplotype segments. LTR retrotransposon families evolved into distinct sub-populations and sub-families that were active in waves lasting several hundred thousand years. Furthermore, It is shown that different retrotransposon sub-families were active in the three wheat sub-genomes, making them useful markers to study and date polyploidization events and chromosomal rearrangements. Additionally, haplotype-specific TE sub-families are used to characterize chromosomal introgressions in different wheat lines. Additionally, populations of non-autonomous TEs co-evolved over millions of years with their autonomous partners, leading to complex systems with multiple types of autonomous, semi-autonomous and non-autonomous elements. Phylogenetic and TE population analyses revealed the relationships between non-autonomous elements and their mobilizing autonomous partners. TE population analysis provided insights into genome evolution of allohexaploid wheat and genetic diversity of species, and may have implication for future crop breeding.
- Published
- 2022
10. A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material
- Author
-
Poretti, Manuel, primary, Praz, Coraline R., additional, Sotiropoulos, Alexandros G., additional, and Wicker, Thomas, additional
- Published
- 2022
- Full Text
- View/download PDF
11. Transposable element populations shed light on the evolutionary history of wheat and the complex co-evolution of autonomous and non-autonomous retrotransposons
- Author
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Wicker, Thomas, Stritt, Christoph, Sotiropoulos, Alexandros G, Poretti, Manuel, Pozniak, Curtis J, Walkowiak, Sean, Gundlach, Heidrun, Stein, Nils, and University of Zurich
- Subjects
UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,10126 Department of Plant and Microbial Biology ,LTR-retrotransposon ,chromosomal introgression ,non-autonomous element ,TE population ,Genetics ,food and beverages ,580 Plants (Botany) ,10211 Zurich-Basel Plant Science Center ,Molecular Biology ,Biochemistry - Abstract
Wheat has one of the largest and most repetitive genomes among major crop plants, containing over 85% transposable elements (TEs). TEs populate genomes much in the way that individuals populate ecosystems, diversifying into different lineages, sub-families and sub-populations. The recent availability of high-quality, chromosome-scale genome sequences from ten wheat lines enables a detailed analysis how TEs evolved in allohexaploid wheat, its diploids progenitors, and in various chromosomal haplotype segments. LTR retrotransposon families evolved into distinct sub-populations and sub-families that were active in waves lasting several hundred thousand years. Furthermore, It is shown that different retrotransposon sub-families were active in the three wheat sub-genomes, making them useful markers to study and date polyploidization events and chromosomal rearrangements. Additionally, haplotype-specific TE sub-families are used to characterize chromosomal introgressions in different wheat lines. Additionally, populations of non-autonomous TEs co-evolved over millions of years with their autonomous partners, leading to complex systems with multiple types of autonomous, semi-autonomous and non-autonomous elements. Phylogenetic and TE population analyses revealed the relationships between non-autonomous elements and their mobilizing autonomous partners. TE population analysis provided insights into genome evolution of allohexaploid wheat and genetic diversity of species, and may have implication for future crop breeding.
- Published
- 2022
12. Comparative genomics and transcriptomics of Triticeae
- Author
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Poretti, Manuel, University of Zurich, and Poretti, Manuel
- Subjects
10126 Department of Plant and Microbial Biology ,UZHDISS UZH Dissertations ,580 Plants (Botany) ,10211 Zurich-Basel Plant Science Center - Published
- 2021
13. Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co‐Evolution of Autonomous and Non‐Autonomous Retrotransposons
- Author
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Wicker, Thomas, primary, Stritt, Christoph, additional, Sotiropoulos, Alexandros G., additional, Poretti, Manuel, additional, Pozniak, Curtis, additional, Walkowiak, Sean, additional, Gundlach, Heidrun, additional, and Stein, Nils, additional
- Published
- 2021
- Full Text
- View/download PDF
14. Comparative Transcriptome Analysis of Wheat Lines in the Field Reveals Multiple Essential Biochemical Pathways Suppressed by Obligate Pathogens
- Author
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Poretti, Manuel, Sotiropoulos, Alexandros G, Graf, Johannes, Jung, Esther, Bourras, Salim, Krattinger, Simon G, Wicker, Thomas, University of Zurich, and Wicker, Thomas
- Subjects
field trial ,10126 Department of Plant and Microbial Biology ,wheat ,1110 Plant Science ,food and beverages ,compatible interaction ,RNA-Seq ,Plant Science ,580 Plants (Botany) ,10211 Zurich-Basel Plant Science Center ,Agricultural Science ,Original Research ,obligate pathogens - Abstract
Mildew and rust are the most devastating cereal pathogens, and in wheat they can cause up to 50% yield loss every year. Wheat lines containing resistance genes are used to effectively control fungal diseases, but the molecular mechanisms underlying the interaction between wheat and its fungal pathogens are poorly understood. Here, we used RNA sequencing (RNA-Seq) to compare the transcriptomic landscape of susceptible and resistant wheat lines to identify genes and pathways that are targeted by obligate biotrophic fungal pathogens. The five lines differed in the expression of thousands of genes under infection as well as control conditions. Generally, mixed infection with powdery mildew and leaf rust resulted in downregulation of numerous genes in susceptible lines. Interestingly, transcriptomic comparison between the nearly isogenic lines Thatcher and Thatcher-Lr34 identified 753 genes that are uniquely downregulated in the susceptible line upon infection. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, revealed the suppression of six major biochemical pathways, namely nuclear transport, alternative splicing, DNA damage response, ubiquitin-mediated proteolysis, phosphoinositol signaling, and photosynthesis. We conclude that powdery mildew and leaf rust evade the wheat defense system by suppression of programmed cell death (PCD) and responses to cellular damage. Considering the broad range of the induced changes, we propose that the pathogen targets “master regulators” at critical steps in the respective pathways. Identification of these wheat genes targeted by the pathogen could inspire new directions for future wheat breeding.
- Published
- 2021
15. A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat
- Author
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Kolodziej, Markus C; https://orcid.org/0000-0003-3155-2935, Singla, Jyoti, Sánchez-Martín, Javier; https://orcid.org/0000-0002-0284-7219, Zbinden, Helen, Šimková, Hana; https://orcid.org/0000-0003-4159-7619, Karafiátová, Miroslava; https://orcid.org/0000-0003-1177-6472, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Gronnier, Julien; https://orcid.org/0000-0002-1429-0542, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Glauser, Gaétan, Zhu, Wangsheng; https://orcid.org/0000-0001-7773-3438, Köster, Philipp; https://orcid.org/0000-0002-1359-822X, Zipfel, Cyril; https://orcid.org/0000-0003-4935-8583, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Kolodziej, Markus C; https://orcid.org/0000-0003-3155-2935, Singla, Jyoti, Sánchez-Martín, Javier; https://orcid.org/0000-0002-0284-7219, Zbinden, Helen, Šimková, Hana; https://orcid.org/0000-0003-4159-7619, Karafiátová, Miroslava; https://orcid.org/0000-0003-1177-6472, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Gronnier, Julien; https://orcid.org/0000-0002-1429-0542, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Glauser, Gaétan, Zhu, Wangsheng; https://orcid.org/0000-0001-7773-3438, Köster, Philipp; https://orcid.org/0000-0002-1359-822X, Zipfel, Cyril; https://orcid.org/0000-0003-4935-8583, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, and Keller, Beat; https://orcid.org/0000-0003-2379-9225
- Abstract
Plasma membrane-associated and intracellular proteins and protein complexes play a pivotal role in pathogen recognition and disease resistance signaling in plants and animals. The two predominant protein families perceiving plant pathogens are receptor-like kinases and nucleotide binding-leucine-rich repeat receptors (NLR), which often confer race-specific resistance. Leaf rust is one of the most prevalent and most devastating wheat diseases. Here, we clone the race-specific leaf rust resistance gene Lr14a from hexaploid wheat. The cloning of Lr14a is aided by the recently published genome assembly of ArinaLrFor, an Lr14a-containing wheat line. Lr14a encodes a membrane-localized protein containing twelve ankyrin (ANK) repeats and structural similarities to Ca2+-permeable non-selective cation channels. Transcriptome analyses reveal an induction of genes associated with calcium ion binding in the presence of Lr14a. Haplotype analyses indicate that Lr14a-containing chromosome segments were introgressed multiple times into the bread wheat gene pool, but we find no variation in the Lr14a coding sequence itself. Our work demonstrates the involvement of an ANK-transmembrane (TM)-like type of gene family in race-specific disease resistance in wheat. This forms the basis to explore ANK-TM-like genes in disease resistance breeding.
- Published
- 2021
16. Comparative Transcriptome Analysis of Wheat Lines in the Field Reveals Multiple Essential Biochemical Pathways Suppressed by Obligate Pathogens
- Author
-
Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Graf, Johannes, Jung, Esther, Bourras, Salim, Krattinger, Simon G, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Graf, Johannes, Jung, Esther, Bourras, Salim, Krattinger, Simon G, and Wicker, Thomas; https://orcid.org/0000-0002-6777-7135
- Abstract
Mildew and rust are the most devastating cereal pathogens, and in wheat they can cause up to 50% yield loss every year. Wheat lines containing resistance genes are used to effectively control fungal diseases, but the molecular mechanisms underlying the interaction between wheat and its fungal pathogens are poorly understood. Here, we used RNA sequencing (RNA-Seq) to compare the transcriptomic landscape of susceptible and resistant wheat lines to identify genes and pathways that are targeted by obligate biotrophic fungal pathogens. The five lines differed in the expression of thousands of genes under infection as well as control conditions. Generally, mixed infection with powdery mildew and leaf rust resulted in downregulation of numerous genes in susceptible lines. Interestingly, transcriptomic comparison between the nearly isogenic lines Thatcher and Thatcher-Lr34 identified 753 genes that are uniquely downregulated in the susceptible line upon infection. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, revealed the suppression of six major biochemical pathways, namely nuclear transport, alternative splicing, DNA damage response, ubiquitin-mediated proteolysis, phosphoinositol signaling, and photosynthesis. We conclude that powdery mildew and leaf rust evade the wheat defense system by suppression of programmed cell death (PCD) and responses to cellular damage. Considering the broad range of the induced changes, we propose that the pathogen targets “master regulators” at critical steps in the respective pathways. Identification of these wheat genes targeted by the pathogen could inspire new directions for future wheat breeding.
- Published
- 2021
17. Domestication of high-copy transposons underlays the wheat small RNA response to an obligate pathogen
- Author
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Gaut, Brandon, Gaut, B ( Brandon ), Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Praz, Coraline Rosalie; https://orcid.org/0000-0002-9133-4406, Meile, Lukas, Kälin, Carol, Schaefer, Luisa Katharina, Schläfli, Michael, Widrig, Victoria, Sanchez-Vallet, Andrea, Wicker, Thomas, Bourras, Salim, Gaut, Brandon, Gaut, B ( Brandon ), Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Praz, Coraline Rosalie; https://orcid.org/0000-0002-9133-4406, Meile, Lukas, Kälin, Carol, Schaefer, Luisa Katharina, Schläfli, Michael, Widrig, Victoria, Sanchez-Vallet, Andrea, Wicker, Thomas, and Bourras, Salim
- Abstract
Plant genomes have evolved several evolutionary mechanisms to tolerate and make use of transposable elements (TEs). Of these, transposon domestication into cis-regulatory and microRNA (miRNA) sequences is proposed to contribute to abiotic/biotic stress adaptation in plants. The wheat genome is derived at 85% from TEs, and contains thousands of miniature inverted-repeat transposable elements (MITEs), whose sequences are particularly prone for domestication into miRNA precursors. In this study, we investigate the contribution of TEs to the wheat small RNA immune response to the lineage-specific, obligate powdery mildew pathogen. We show that MITEs of the Mariner superfamily contribute the largest diversity of miRNAs to the wheat immune response. In particular, MITE precursors of miRNAs are wide-spread over the wheat genome, and highly conserved copies are found in the Lr34 and QPm.tut-4A mildew resistance loci. Our work suggests that transposon domestication is an important evolutionary force driving miRNA functional innovation in wheat immunity.
- Published
- 2020
18. A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew
- Author
-
Müller, Marion C; https://orcid.org/0000-0001-5594-2319, Praz, Coraline R; https://orcid.org/0000-0002-9133-4406, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Menardo, Fabrizio; https://orcid.org/0000-0002-7885-4482, Kunz, Lukas; https://orcid.org/0000-0002-8155-5408, Schudel, Seraina; https://orcid.org/0000-0003-3999-843X, Oberhänsli, Simone, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Wehrli, Andreas; https://orcid.org/0000-0001-9110-8508, Bourras, Salim; https://orcid.org/0000-0003-0855-5433, Keller, Beat; https://orcid.org/0000-0003-2379-9225, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Müller, Marion C; https://orcid.org/0000-0001-5594-2319, Praz, Coraline R; https://orcid.org/0000-0002-9133-4406, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Menardo, Fabrizio; https://orcid.org/0000-0002-7885-4482, Kunz, Lukas; https://orcid.org/0000-0002-8155-5408, Schudel, Seraina; https://orcid.org/0000-0003-3999-843X, Oberhänsli, Simone, Poretti, Manuel; https://orcid.org/0000-0001-6915-2238, Wehrli, Andreas; https://orcid.org/0000-0001-9110-8508, Bourras, Salim; https://orcid.org/0000-0003-0855-5433, Keller, Beat; https://orcid.org/0000-0003-2379-9225, and Wicker, Thomas; https://orcid.org/0000-0002-6777-7135
- Abstract
Blumeria graminis f. sp. tritici (B.g. tritici) is the causal agent of the wheat powdery mildew disease. The highly fragmented B.g. tritici genome available so far has prevented a systematic analysis of effector genes that are known to be involved in host adaptation. To study the diversity and evolution of effector genes we produced a chromosome‐scale assembly of the B.g. tritici genome. The genome assembly and annotation was achieved by combining long‐read sequencing with high‐density genetic mapping, bacterial artificial chromosome fingerprinting and transcriptomics. We found that the 166.6 Mb B.g. tritici genome encodes 844 candidate effector genes, over 40% more than previously reported. Candidate effector genes have characteristic local genomic organization such as gene clustering and enrichment for recombination‐active regions and certain transposable element families. A large group of 412 candidate effector genes shows high plasticity in terms of copy number variation in a global set of 36 isolates and of transcription levels. Our data suggest that copy number variation and transcriptional flexibility are the main drivers for adaptation in B.g. tritici. The high repeat content may play a role in providing a genomic environment that allows rapid evolution of effector genes with selection as the driving force.
- Published
- 2019
19. Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen
- Author
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Poretti, Manuel, primary, Praz, Coraline Rosalie, primary, Meile, Lukas, primary, Kälin, Carol, primary, Schaefer, Luisa Katharina, primary, Schläfli, Michael, primary, Widrig, Victoria, primary, Sanchez-Vallet, Andrea, primary, Wicker, Thomas, primary, and Bourras, Salim, primary
- Published
- 2019
- Full Text
- View/download PDF
20. Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen.
- Author
-
Poretti, Manuel, Praz, Coraline Rosalie, Meile, Lukas, Kälin, Carol, Schaefer, Luisa Katharina, Schläfli, Michael, Widrig, Victoria, Sanchez-Vallet, Andrea, Wicker, Thomas, and Bourras, Salim
- Abstract
Plant genomes have evolved several evolutionary mechanisms to tolerate and make use of transposable elements (TEs). Of these, transposon domestication into cis-regulatory and microRNA (miRNA) sequences is proposed to contribute to abiotic/biotic stress adaptation in plants. The wheat genome is derived at 85% from TEs, and contains thousands of miniature inverted-repeat transposable elements (MITEs), whose sequences are particularly prone for domestication into miRNA precursors. In this study, we investigate the contribution of TEs to the wheat small RNA immune response to the lineage-specific, obligate powdery mildew pathogen. We show that MITEs of the Mariner superfamily contribute the largest diversity of miRNAs to the wheat immune response. In particular, MITE precursors of miRNAs are wide-spread over the wheat genome, and highly conserved copies are found in the Lr34 and QPm.tut-4A mildew resistance loci. Our work suggests that transposon domestication is an important evolutionary force driving miRNA functional innovation in wheat immunity. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
21. A chromosome‐scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew
- Author
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Müller, Marion C., primary, Praz, Coraline R., additional, Sotiropoulos, Alexandros G., additional, Menardo, Fabrizio, additional, Kunz, Lukas, additional, Schudel, Seraina, additional, Oberhänsli, Simone, additional, Poretti, Manuel, additional, Wehrli, Andreas, additional, Bourras, Salim, additional, Keller, Beat, additional, and Wicker, Thomas, additional
- Published
- 2018
- Full Text
- View/download PDF
22. Domestication of high-copy transposons underlays the wheat small RNA response to an obligate pathogen
- Author
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Poretti, Manuel, Praz, Coraline R., Meile, Lukas, Kälin, Carol, Schaefer, Luisa K., Schläfli, Michael, Widrig, Victoria, Sánchez-Vallet, Andrea, Wicker, Thomas, and Bourras, Salim
- Subjects
2. Zero hunger ,Powdery mildew ,small RNAs ,Wheat ,food and beverages ,Transposable elements - Abstract
Plant genomes have evolved several evolutionary mechanisms to tolerate and make use of transposable elements (TEs). Of these, transposon domestication into cis-regulatory and microRNA (miRNA) sequences is proposed to contribute to abiotic/biotic stress adaptation in plants. The wheat genome is derived at 85% from TEs, and contains thousands of miniature inverted-repeat transposable elements (MITEs), whose sequences are particularly prone for domestication into miRNA precursors. In this study, we investigate the contribution of TEs to the wheat small RNA immune response to the lineage-specific, obligate powdery mildew pathogen. We show that MITEs of the Mariner superfamily contribute the largest diversity of miRNAs to the wheat immune response. In particular, MITE precursors of miRNAs are wide-spread over the wheat genome, and highly conserved copies are found in the Lr34 and QPm.tut-4A mildew resistance loci. Our work suggests that transposon domestication is an important evolutionary force driving miRNA functional innovation in wheat immunity., Molecular Biology and Evolution, 37 (3), ISSN:0737-4038, ISSN:1537-1719
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