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2. Structural variation in the pangenome of wild and domesticated barley

Author

Jayakodi, Murukarthick, Lu, Qiongxian, Pidon, Hélène, Rabanus-Wallace, M. Timothy, Bayer, Micha, Lux, Thomas, Guo, Yu, Jaegle, Benjamin, Badea, Ana, Bekele, Wubishet, Brar, Gurcharn S., Braune, Katarzyna, Bunk, Boyke, Chalmers, Kenneth J., Chapman, Brett, Jørgensen, Morten Egevang, Feng, Jia-Wu, Feser, Manuel, Fiebig, Anne, Gundlach, Heidrun, Guo, Wenbin, Haberer, Georg, Hansson, Mats, Himmelbach, Axel, Hoffie, Iris, Hoffie, Robert E., Hu, Haifei, Isobe, Sachiko, König, Patrick, Kale, Sandip M., Kamal, Nadia, Keeble-Gagnère, Gabriel, Keller, Beat, Knauft, Manuela, Koppolu, Ravi, Krattinger, Simon G., Kumlehn, Jochen, Langridge, Peter, Li, Chengdao, Marone, Marina P., Maurer, Andreas, Mayer, Klaus F. X., Melzer, Michael, Muehlbauer, Gary J., Murozuka, Emiko, Padmarasu, Sudharsan, Perovic, Dragan, Pillen, Klaus, Pin, Pierre A., Pozniak, Curtis J., Ramsay, Luke, Pedas, Pai Rosager, Rutten, Twan, Sakuma, Shun, Sato, Kazuhiro, Schüler, Danuta, Schmutzer, Thomas, Scholz, Uwe, Schreiber, Miriam, Shirasawa, Kenta, Simpson, Craig, Skadhauge, Birgitte, Spannagl, Manuel, Steffenson, Brian J., Thomsen, Hanne C., Tibbits, Josquin F., Nielsen, Martin Toft Simmelsgaard, Trautewig, Corinna, Vequaud, Dominique, Voss, Cynthia, Wang, Penghao, Waugh, Robbie, Westcott, Sharon, Rasmussen, Magnus Wohlfahrt, Zhang, Runxuan, Zhang, Xiao-Qi, Wicker, Thomas, Dockter, Christoph, Mascher, Martin, and Stein, Nils

Published
2024
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4. Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation

Author

Russo, Alessia, Alessandrini, Mattia, El Baidouri, Moaine, Frei, Daniel, Galise, Teresa Rosa, Gaidusch, Lara, Oertel, Hannah F., Garcia Morales, Sara E., Potente, Giacomo, Tian, Qin, Smetanin, Dmitry, Bertrand, Joris A. M., Onstein, Renske E., Panaud, Olivier, Frey, Jürg E., Cozzolino, Salvatore, Wicker, Thomas, Xu, Shuqing, Grossniklaus, Ueli, and Schlüter, Philipp M.

Published
2024
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6. Einkorn genomics sheds light on history of the oldest domesticated wheat

Author

Ahmed, Hanin Ibrahim, Heuberger, Matthias, Schoen, Adam, Koo, Dal-Hoe, Quiroz-Chavez, Jesus, Adhikari, Laxman, Raupp, John, Cauet, Stéphane, Rodde, Nathalie, Cravero, Charlotte, Callot, Caroline, Lazo, Gerard R., Kathiresan, Nagarajan, Sharma, Parva K., Moot, Ian, Yadav, Inderjit Singh, Singh, Lovepreet, Saripalli, Gautam, Rawat, Nidhi, Datla, Raju, Athiyannan, Naveenkumar, Ramirez-Gonzalez, Ricardo H., Uauy, Cristobal, Wicker, Thomas, Tiwari, Vijay K., Abrouk, Michael, Poland, Jesse, and Krattinger, Simon G.

Published
2023
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8. A fatty acid anabolic pathway in specialized-cells sustains a remote signal that controls egg activation in Drosophila.

Author

Mickael Poidevin, Nicolas Mazuras, Gwénaëlle Bontonou, Pierre Delamotte, Béatrice Denis, Maëlle Devilliers, Perla Akiki, Delphine Petit, Laura de Luca, Priscilla Soulie, Cynthia Gillet, Claude Wicker-Thomas, and Jacques Montagne

Subjects
Genetics, QH426-470
Abstract

Egg activation, representing the critical oocyte-to-embryo transition, provokes meiosis completion, modification of the vitelline membrane to prevent polyspermy, and translation of maternally provided mRNAs. This transition is triggered by a calcium signal induced by spermatozoon fertilization in most animal species, but not in insects. In Drosophila melanogaster, mature oocytes remain arrested at metaphase-I of meiosis and the calcium-dependent activation occurs while the oocyte moves through the genital tract. Here, we discovered that the oenocytes of fruitfly females are required for egg activation. Oenocytes, cells specialized in lipid-metabolism, are located beneath the abdominal cuticle. In adult flies, they synthesize the fatty acids (FAs) that are the precursors of cuticular hydrocarbons (CHCs), including pheromones. The oenocyte-targeted knockdown of a set of FA-anabolic enzymes, involved in very-long-chain fatty acid (VLCFA) synthesis, leads to a defect in egg activation. Given that some but not all of the identified enzymes are required for CHC/pheromone biogenesis, this putative VLCFA-dependent remote control may rely on an as-yet unidentified CHC or may function in parallel to CHC biogenesis. Additionally, we discovered that the most posterior ventral oenocyte cluster is in close proximity to the uterus. Since oocytes dissected from females deficient in this FA-anabolic pathway can be activated in vitro, this regulatory loop likely operates upstream of the calcium trigger. To our knowledge, our findings provide the first evidence that a physiological extra-genital signal remotely controls egg activation. Moreover, our study highlights a potential metabolic link between pheromone-mediated partner recognition and egg activation.

Published
2024
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11. Multiple wheat genomes reveal global variation in modern breeding

Author

Walkowiak, Sean, Gao, Liangliang, Monat, Cecile, Haberer, Georg, Kassa, Mulualem T, Brinton, Jemima, Ramirez-Gonzalez, Ricardo H, Kolodziej, Markus C, Delorean, Emily, Thambugala, Dinushika, Klymiuk, Valentyna, Byrns, Brook, Gundlach, Heidrun, Bandi, Venkat, Siri, Jorge Nunez, Nilsen, Kirby, Aquino, Catharine, Himmelbach, Axel, Copetti, Dario, Ban, Tomohiro, Venturini, Luca, Bevan, Michael, Clavijo, Bernardo, Koo, Dal-Hoe, Ens, Jennifer, Wiebe, Krystalee, N’Diaye, Amidou, Fritz, Allen K, Gutwin, Carl, Fiebig, Anne, Fosker, Christine, Fu, Bin Xiao, Accinelli, Gonzalo Garcia, Gardner, Keith A, Fradgley, Nick, Gutierrez-Gonzalez, Juan, Halstead-Nussloch, Gwyneth, Hatakeyama, Masaomi, Koh, Chu Shin, Deek, Jasline, Costamagna, Alejandro C, Fobert, Pierre, Heavens, Darren, Kanamori, Hiroyuki, Kawaura, Kanako, Kobayashi, Fuminori, Krasileva, Ksenia, Kuo, Tony, McKenzie, Neil, Murata, Kazuki, Nabeka, Yusuke, Paape, Timothy, Padmarasu, Sudharsan, Percival-Alwyn, Lawrence, Kagale, Sateesh, Scholz, Uwe, Sese, Jun, Juliana, Philomin, Singh, Ravi, Shimizu-Inatsugi, Rie, Swarbreck, David, Cockram, James, Budak, Hikmet, Tameshige, Toshiaki, Tanaka, Tsuyoshi, Tsuji, Hiroyuki, Wright, Jonathan, Wu, Jianzhong, Steuernagel, Burkhard, Small, Ian, Cloutier, Sylvie, Keeble-Gagnère, Gabriel, Muehlbauer, Gary, Tibbets, Josquin, Nasuda, Shuhei, Melonek, Joanna, Hucl, Pierre J, Sharpe, Andrew G, Clark, Matthew, Legg, Erik, Bharti, Arvind, Langridge, Peter, Hall, Anthony, Uauy, Cristobal, Mascher, Martin, Krattinger, Simon G, Handa, Hirokazu, Shimizu, Kentaro K, Distelfeld, Assaf, Chalmers, Ken, Keller, Beat, Mayer, Klaus FX, Poland, Jesse, Stein, Nils, McCartney, Curt A, Spannagl, Manuel, Wicker, Thomas, and Pozniak, Curtis J

Subjects
Genetics, Biotechnology, Human Genome, Acclimatization, Animals, Centromere, Chromosome Mapping, Cloning, Molecular, DNA Copy Number Variations, DNA Transposable Elements, Edible Grain, Genes, Plant, Genetic Introgression, Genetic Variation, Genome, Plant, Genomics, Haplotypes, Insecta, Internationality, NLR Proteins, Plant Breeding, Plant Diseases, Plant Proteins, Polymorphism, Single Nucleotide, Polyploidy, Triticum, General Science & Technology
Abstract

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Published
2020

12. A fictional field case study to understand the genetic basis of host-fungal pathogen interactions using the wheat powdery mildew-wheat pathosystem.

Author

Sotiropoulos, Alexandros G., Sánchez-Martín, Javier, Widrig, Victoria, Isaksson, Jonatan, Bernasconi, Zoe, Koller, Teresa, Bearth, Giulia, Herren, Gerhard, Wicker, Thomas, and Keller, Beat

Subjects
DISEASE resistance of plants, PATHOGENIC fungi, ERYSIPHE graminis, PHYTOPATHOGENIC fungi, PLANT-fungus relationships, POWDERY mildew diseases
Abstract

Wheat powdery mildew is an important fungal pathogen of wheat with an obligatory biotrophic lifestyle (a parasite that can only develop on a living host). We investigated the genetics of this host-pathogen interaction by using phenotyping and PCR assays to detect genes in both wheat and powdery mildew, which are known determinants of the outcome of these interactions (resistance or susceptibility). The mildew genes increase or decrease the pathogen virulence, while the wheat genes provide specific immunity against the mildew isolates expressing the corresponding avirulence genes. Here, we describe the experiments performed to understand the genetic basis of race-specific resistance of wheat to powdery mildew, which is part of the course 'Mechanisms of Plant Disease Resistance against Fungal Pathogens' designed for advanced third-year students of biology at the University of Zurich, Switzerland. In this course, students learn how plants and their pathogenic fungi engage in an arms race against each other to survive. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Author

Stein, Joshua C, Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J, Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos EM, Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty SS, Talag, Jayson, Danowitz, Ann, Rivera, Luis F, Gschwend, Andrea R, Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, Rosa Farias, Daniel da, da Maia, Luciano Carlos, dos Santos, Railson S, Nyberg, Kevin G, McNally, Kenneth L, Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K, Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C, Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A, Machado, Carlos A, Sanderson, Michael J, Long, Manyuan, Ware, Doreen, and Wing, Rod A

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Conserved Sequence, Crops, Agricultural, Domestication, Evolution, Molecular, Genetic Speciation, Genetic Variation, Genome, Plant, Oryza, Phylogeny, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

Published
2018

14. Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade

Author

Sotiropoulos, Alexandros G., Arango-Isaza, Epifanía, Ban, Tomohiro, Barbieri, Chiara, Bourras, Salim, Cowger, Christina, Czembor, Paweł C., Ben-David, Roi, Dinoor, Amos, Ellwood, Simon R., Graf, Johannes, Hatta, Koichi, Helguera, Marcelo, Sánchez-Martín, Javier, McDonald, Bruce A., Morgounov, Alexey I., Müller, Marion C., Shamanin, Vladimir, Shimizu, Kentaro K., Yoshihira, Taiki, Zbinden, Helen, Keller, Beat, and Wicker, Thomas

Published
2022
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15. Atlas of tandem kinase proteins across the plant kingdom

Author

Fahima, Tzion, primary, Reveguk, Tamara, additional, Fatiukha, Andrii, additional, Potapenko, Evgenii, additional, Reveguk, Ivan, additional, Sela, Hanan, additional, Klymiuk, Valentyna, additional, Li, Yinghui, additional, Pozniak, Curtis, additional, Wicker, Thomas, additional, and Coaker, Gitta, additional

Published
2024
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17. Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the Mediterranean grass Brachypodium distachyon

Author

Stritt, Christoph, Gordon, Sean P, Wicker, Thomas, Vogel, John P, and Roulin, Anne C

Subjects
Biotechnology, Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Brachypodium, DNA Transposable Elements, DNA, Plant, Ecosystem, Evolution, Molecular, Gene Frequency, Genetic Drift, Genetic Variation, Genome, Plant, Mediterranean Region, Phylogeny, Polymorphism, Genetic, Selection, Genetic, genetic variation, retrotransposons, DNA transposons, natural populations, demographic history, Biochemistry and Cell Biology, Evolutionary Biology, Developmental Biology
Abstract

Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are "well-behaved" compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.

Published
2018

18. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Author

Luo, Ming-Cheng, Gu, Yong Q, Puiu, Daniela, Wang, Hao, Twardziok, Sven O, Deal, Karin R, Huo, Naxin, Zhu, Tingting, Wang, Le, Wang, Yi, McGuire, Patrick E, Liu, Shuyang, Long, Hai, Ramasamy, Ramesh K, Rodriguez, Juan C, Van, Sonny L, Yuan, Luxia, Wang, Zhenzhong, Xia, Zhiqiang, Xiao, Lichan, Anderson, Olin D, Ouyang, Shuhong, Liang, Yong, Zimin, Aleksey V, Pertea, Geo, Qi, Peng, Bennetzen, Jeffrey L, Dai, Xiongtao, Dawson, Matthew W, Müller, Hans-Georg, Kugler, Karl, Rivarola-Duarte, Lorena, Spannagl, Manuel, Mayer, Klaus FX, Lu, Fu-Hao, Bevan, Michael W, Leroy, Philippe, Li, Pingchuan, You, Frank M, Sun, Qixin, Liu, Zhiyong, Lyons, Eric, Wicker, Thomas, Salzberg, Steven L, Devos, Katrien M, and Dvořák, Jan

Subjects
Biological Sciences, Genetics, Human Genome, Stem Cell Research, Stem Cell Research - Nonembryonic - Non-Human, Chromosome Mapping, Diploidy, Evolution, Molecular, Gene Duplication, Genes, Plant, Genome, Plant, Genomics, Phylogeny, Poaceae, Recombination, Genetic, Sequence Analysis, DNA, Triticum, General Science & Technology
Abstract

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

Published
2017

19. A chromosome conformation capture ordered sequence of the barley genome

Author

Mascher, Martin, Gundlach, Heidrun, Himmelbach, Axel, Beier, Sebastian, Twardziok, Sven O, Wicker, Thomas, Radchuk, Volodymyr, Dockter, Christoph, Hedley, Pete E, Russell, Joanne, Bayer, Micha, Ramsay, Luke, Liu, Hui, Haberer, Georg, Zhang, Xiao-Qi, Zhang, Qisen, Barrero, Roberto A, Li, Lin, Taudien, Stefan, Groth, Marco, Felder, Marius, Hastie, Alex, Šimková, Hana, Staňková, Helena, Vrána, Jan, Chan, Saki, Muñoz-Amatriaín, María, Ounit, Rachid, Wanamaker, Steve, Bolser, Daniel, Colmsee, Christian, Schmutzer, Thomas, Aliyeva-Schnorr, Lala, Grasso, Stefano, Tanskanen, Jaakko, Chailyan, Anna, Sampath, Dharanya, Heavens, Darren, Clissold, Leah, Cao, Sujie, Chapman, Brett, Dai, Fei, Han, Yong, Li, Hua, Li, Xuan, Lin, Chongyun, McCooke, John K, Tan, Cong, Wang, Penghao, Wang, Songbo, Yin, Shuya, Zhou, Gaofeng, Poland, Jesse A, Bellgard, Matthew I, Borisjuk, Ljudmilla, Houben, Andreas, Doležel, Jaroslav, Ayling, Sarah, Lonardi, Stefano, Kersey, Paul, Langridge, Peter, Muehlbauer, Gary J, Clark, Matthew D, Caccamo, Mario, Schulman, Alan H, Mayer, Klaus FX, Platzer, Matthias, Close, Timothy J, Scholz, Uwe, Hansson, Mats, Zhang, Guoping, Braumann, Ilka, Spannagl, Manuel, Li, Chengdao, Waugh, Robbie, and Stein, Nils

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Cell Nucleus, Centromere, Chromatin, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Chromosomes, Plant, Genetic Variation, Genome, Plant, Genomics, Haplotypes, Hordeum, Meiosis, Repetitive Sequences, Nucleic Acid, Seeds, General Science & Technology
Abstract

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Published
2017

21. A fatty acid anabolic pathway in specialized-cells sustains a remote signal that controls egg activation in Drosophila

Author

Poidevin, Mickael, primary, Mazuras, Nicolas, additional, Bontonou, Gwénaëlle, additional, Delamotte, Pierre, additional, Denis, Béatrice, additional, Devilliers, Maëlle, additional, Akiki, Perla, additional, Petit, Delphine, additional, de Luca, Laura, additional, Soulie, Priscilla, additional, Gillet, Cynthia, additional, Wicker-Thomas, Claude, additional, and Montagne, Jacques, additional

Published
2024
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23. Adaptive diversification through structural variation in barley

Author

Jayakodi, Murukarthick, primary, Lu, Qiongxian, additional, Pidon, Helene, additional, Rabanus-Wallace, M. Timothy, additional, Bayer, Micha, additional, Lux, Thomas, additional, Guo, Yu, additional, Jaegle, Benjamin, additional, Badea, Ana, additional, Bekele, Wubishet, additional, Brar, Gurcharn, additional, Braune, Katarzyna, additional, Bunk, Boyke, additional, Chalmers, Kenneth, additional, Chapman, Brett, additional, Jorgensen, Morten Egevang, additional, Feng, Jia-Wu, additional, Feser, Manuel, additional, Fiebig, Anne, additional, Gundlach, Heidrun, additional, Guo, Wenbin, additional, Haberer, Georg, additional, Hansson, Mats, additional, Himmelbach, Axel, additional, Hoffie, Iris, additional, Hoffie, Robert, additional, Hu, Haifei, additional, Isobe, Sachiko, additional, Koenig, Patrick, additional, Kale, Sandip, additional, Kamal, Nadia, additional, Keeble-Gagnere, Gabriel, additional, Keller, Beat, additional, Knauft, Manuela, additional, Koppolu, Ravi, additional, Krattinger, Simon, additional, Kumlehn, Jochen, additional, Langridge, Peter, additional, Li, Chengdao, additional, Marone, Marina, additional, Maurer, Andreas, additional, Mayer, Klaus, additional, Melzer, Michael, additional, Muehlbauer, Gary, additional, Murozuka, Emiko, additional, Padmarasu, Sudharsan, additional, Perovic, Dragan, additional, Pillen, Klaus, additional, Pin, Pierre, additional, Pozniak, Curtis, additional, Ramsay, Luke, additional, Pedas, Pai Rosager, additional, Rutten, Twan, additional, Sakuma, Shun, additional, Sato, Kazuhiro, additional, Schueler, Danuta, additional, Schmutzer, Thomas, additional, Scholz, Uwe, additional, Schreiber, Miriam, additional, Shirasawa, Kenta, additional, Simpson, Craig, additional, Skadhauge, Birgitte, additional, Spannagl, Manuel, additional, Steffenson, Brian, additional, Thomsen, Hanne, additional, Tibbits, Josquin, additional, Nielsen, Martin Toft Simmelsgaard, additional, Trautewig, Corinna, additional, Vequaud, Dominique, additional, Voss, Cynthia, additional, Wang, Penghao, additional, Waugh, Robbie, additional, Westcott, Sharon, additional, Rasmussen, Magnus Wohlfahrt, additional, Zhang, Runxuan, additional, Zhang, Xiao-Qi, additional, Wicker, Thomas, additional, Dockter, Christoph, additional, Mascher, Martin, additional, and Stein, Nils, additional

Published
2024
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24. Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Author

Rabanus-Wallace, M. Timothy, Hackauf, Bernd, Mascher, Martin, Lux, Thomas, Wicker, Thomas, Gundlach, Heidrun, Baez, Mariana, Houben, Andreas, Mayer, Klaus F. X., Guo, Liangliang, Poland, Jesse, Pozniak, Curtis J., Walkowiak, Sean, Melonek, Joanna, Praz, Coraline R., Schreiber, Mona, Budak, Hikmet, Heuberger, Matthias, Steuernagel, Burkhard, Wulff, Brande, Börner, Andreas, Byrns, Brook, Čížková, Jana, Fowler, D. Brian, Fritz, Allan, Himmelbach, Axel, Kaithakottil, Gemy, Keilwagen, Jens, Keller, Beat, Konkin, David, Larsen, Jamie, Li, Qiang, Myśków, Beata, Padmarasu, Sudharsan, Rawat, Nidhi, Sesiz, Uğur, Biyiklioglu-Kaya, Sezgi, Sharpe, Andy, Šimková, Hana, Small, Ian, Swarbreck, David, Toegelová, Helena, Tsvetkova, Natalia, Voylokov, Anatoly V., Vrána, Jan, Bauer, Eva, Bolibok-Bragoszewska, Hanna, Doležel, Jaroslav, Hall, Anthony, Jia, Jizeng, Korzun, Viktor, Laroche, André, Ma, Xue-Feng, Ordon, Frank, Özkan, Hakan, Rakoczy-Trojanowska, Monika, Scholz, Uwe, Schulman, Alan H., Siekmann, Dörthe, Stojałowski, Stefan, Tiwari, Vijay K., Spannagl, Manuel, and Stein, Nils

Published
2021
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28. Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX/RALF/FER growth regulatory module

Author

Gupta, Shibu; https://orcid.org/0000-0003-0412-7423, Guérin, Amandine; https://orcid.org/0000-0001-7143-5042, Herger, Aline; https://orcid.org/0000-0003-1043-6441, Hou, Xiaoyu; https://orcid.org/0009-0000-0216-4648, Schaufelberger, Myriam; https://orcid.org/0000-0003-4060-7870, Roulard, Romain; https://orcid.org/0000-0002-3200-7130, Diet, Anouck; https://orcid.org/0009-0002-7612-4168, Roffler, Stefan, Lefebvre, Valérie; https://orcid.org/0000-0003-4482-3810, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Pelloux, Jérôme; https://orcid.org/0000-0002-9371-1711, Ringli, Christoph; https://orcid.org/0000-0002-5533-2235, Gupta, Shibu; https://orcid.org/0000-0003-0412-7423, Guérin, Amandine; https://orcid.org/0000-0001-7143-5042, Herger, Aline; https://orcid.org/0000-0003-1043-6441, Hou, Xiaoyu; https://orcid.org/0009-0000-0216-4648, Schaufelberger, Myriam; https://orcid.org/0000-0003-4060-7870, Roulard, Romain; https://orcid.org/0000-0002-3200-7130, Diet, Anouck; https://orcid.org/0009-0002-7612-4168, Roffler, Stefan, Lefebvre, Valérie; https://orcid.org/0000-0003-4482-3810, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Pelloux, Jérôme; https://orcid.org/0000-0002-9371-1711, and Ringli, Christoph; https://orcid.org/0000-0002-5533-2235

Abstract

Plant cell growth involves coordination of numerous processes and signaling cascades among the different cellular compartments to concomitantly enlarge the protoplast and the surrounding cell wall. The cell wall integrity-sensing process involves the extracellular LRX (LRR-Extensin) proteins that bind RALF (Rapid ALkalinization Factor) peptide hormones and, in vegetative tissues, interact with the transmembrane receptor kinase FERONIA (FER). This LRX/RALF/FER signaling module influences cell wall composition and regulates cell growth. The numerous proteins involved in or influenced by this module are beginning to be characterized. In a genetic screen, mutations in Apyrase 7 (APY7) were identified to suppress growth defects observed in lrx1 and fer mutants. APY7 encodes a Golgi-localized NTP-diphosphohydrolase, but opposed to other apyrases of Arabidopsis, APY7 revealed to be a negative regulator of cell growth. APY7 modulates the growth-inhibiting effect of RALF1, influences the cell wall architecture and -composition, and alters the pH of the extracellular matrix, all of which affect cell growth. Together, this study reveals a function of APY7 in cell wall formation and cell growth that is connected to growth processes influenced by the LRX/RALF/FER signaling module.

Published
2024

30. A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material

Author

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

31. Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX/RALF/FER growth regulatory module

Author

Gupta, Shibu, primary, Guérin, Amandine, additional, Herger, Aline, additional, Hou, Xiaoyu, additional, Schaufelberger, Myriam, additional, Roulard, Romain, additional, Diet, Anouck, additional, Roffler, Stefan, additional, Lefebvre, Valérie, additional, Wicker, Thomas, additional, Pelloux, Jérôme, additional, and Ringli, Christoph, additional

Published
2024
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32. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

Author

Wang, Muhua, Yu, Yeisoo, Haberer, Georg, Marri, Pradeep Reddy, Fan, Chuanzhu, Goicoechea, Jose Luis, Zuccolo, Andrea, Song, Xiang, Kudrna, Dave, Ammiraju, Jetty SS, Cossu, Rosa Maria, Maldonado, Carlos, Chen, Jinfeng, Lee, Seunghee, Sisneros, Nick, de Baynast, Kristi, Golser, Wolfgang, Wissotski, Marina, Kim, Woojin, Sanchez, Paul, Ndjiondjop, Marie-Noelle, Sanni, Kayode, Long, Manyuan, Carney, Judith, Panaud, Olivier, Wicker, Thomas, Machado, Carlos A, Chen, Mingsheng, Mayer, Klaus FX, Rounsley, Steve, and Wing, Rod A

Subjects
Africa, Amino Acid Sequence, Base Sequence, Crops, Agricultural, DNA, Plant, Genetic Variation, Genetics, Population, Genome, Plant, Molecular Sequence Data, Oryza, Sequence Analysis, DNA, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

Published
2014

33. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Author

Consortium, The International Wheat Genome Sequencing, Mayer, Klaus FX, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J, Sourdille, Pierre, Endo, Takashi R, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, McLay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Sandve, Simen Rød, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Pfeifer, Matthias, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikaël, Keller, Beat, and Praud, Sebastien

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Human Genome, Bread, Chromosomes, Plant, Evolution, Molecular, Gene Order, Genetic Variation, Genome, Plant, Molecular Sequence Annotation, Phylogeny, Plant Proteins, Polyploidy, Sequence Analysis, DNA, Transcriptome, Triticum, International Wheat Genome Sequencing Consortium, General Science & Technology
Abstract

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Published
2014

35. List of contributors

Author

Anderson, Alisha R., primary, Andersson, Martin N., additional, Ashourian, Kristen Taylor, additional, Blomquist, Gary J., additional, Bruckmann, Astrid, additional, Chertemps, Thomas, additional, Crewe, Robin M., additional, Fandino, Richard A., additional, Ferguson, Stephen T., additional, Fleischer, Jörg, additional, Ginzel, Matthew D., additional, Hansson, Bill S., additional, Hofferberth, John, additional, Jacquin-Joly, Emmanuelle, additional, Jurenka, R.A., additional, Kanzaki, Ryohei, additional, Keeling, Christopher I., additional, Keesey, Ian W., additional, Krieger, Jürgen, additional, Löfstedt, Christer, additional, MacLean, Marina, additional, Maïbèche, Martine, additional, Miazzi, Fabio, additional, Mitchell, Robert F., additional, Mitsuno, Hidefumi, additional, Montagne, Jacques, additional, Montagné, Nicolas, additional, Mumoki, Fiona N., additional, Namiki, Shigehiro, additional, Newcomb, Richard D., additional, Pinnelli, Govardhana R., additional, Plettner, Erika, additional, Ray, Anandasankar, additional, Ruther, Joachim, additional, Sakurai, Takeshi, additional, Schröder, Katrin, additional, Sparks, Jackson T., additional, Stengl, Monika, additional, Terrado, Mailyn, additional, Tholl, Dorothea, additional, Tittiger, Claus, additional, Vogt, Richard G., additional, Wanner, Kevin, additional, Wicher, Dieter, additional, Wicker-Thomas, Claude, additional, Xia, Yi-Han, additional, and Zwiebel, Laurence J., additional

Published
2021
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36. The genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and adaptation to pollinators

Author

Schlüter, Philipp, primary, Russo, Alessia, additional, Alessandrini, Mattia, additional, Baidouri, Moaine El, additional, Frei, Daniel, additional, Galise, Teresa, additional, Gaidusch, Lara, additional, Oertel, Hannah, additional, Morales, Sara Garcia, additional, Potente, Giacomo, additional, Tian, Qin, additional, Smetanin, Dmitry, additional, Bertrand, Joris, additional, Onstein, Renske, additional, Panaud, Olivier, additional, Frey, Jürg, additional, Cozzolino, Salvatore, additional, Wicker, Thomas, additional, Xu, Shuqing, additional, and Grossniklaus, Ueli, additional

Published
2023
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40. The Sorghum bicolor genome and the diversification of grasses

Author

Paterson, Andrew H., Bowers, John E., Bruggmann, Remy, dubchak, Inna, Grimwood, Jane, Gundlach, Heidrun, Haberer, Georg, Hellsten, Uffe, Mitros, Therese, Poliakov, Alexander, Schmutz, Jeremy, Spannagl, Manuel, Tang, Haibo, Wang, Xiyin, Wicker, Thomas, Bharti, Arvind K., Chapman, Jarrod, Feltus, F. Alex, Gowik, Udo, Grigoriev, Igor V., Lyons, Eric, Maher, Christopher A., Martis, Mihaela, Marechania, Apurva, Otillar, Robert P., Penning, Bryan W., Salamov, Asaf. A., Wang, Yu, Zhang, Lifang, Carpita, Nicholas C., Freeling, Michael, Gingle, Alan R., hash, C. Thomas, Keller, Beat, Klein, Patricia, Kresovich, Stephen, McCann, Maureen C., Ming, Ray, Peterson, Daniel G., ur-Rahman, Mehboob-, Ware, Doreen, Westhoff, Peter, Mayer, Klaus F. X., Messing, Joachim, and Rokhsar, Daniel S.

Abstract

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approx730-megabase Sorghum bicolor (L.) Moench genome, placing approx98percent of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approx75percent larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approx70 million years ago, most duplicated gene sets lost one member before the sorghum rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24percent of genes are grass-specific and 7percent are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Published
2009

45. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author

Abrouk, Michael, Ahmed, Hanin Ibrahim, Cubry, Philippe, Šimoníková, Denisa, Cauet, Stéphane, Pailles, Yveline, Bettgenhaeuser, Jan, Gapa, Liubov, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leila, Kathiresan, Nagarajan, Čížková, Jana, Hřibová, Eva, Doležel, Jaroslav, Arribat, Sandrine, Bergès, Hélène, Wieringa, Jan J., Gueye, Mathieu, Kane, Ndjido A., Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas, Vigouroux, Yves, Barnaud, Adeline, and Krattinger, Simon G.

Published
2020
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46. A fictional field case study to understand the genetic basis of host-fungal pathogen interactions using the wheat powdery mildew-wheat pathosystem

Author

Sotiropoulos, Alexandros G, Sánchez-Martín, Javier, Widrig, Victoria, Isaksson, Jonatan, Bernasconi, Zoe, Koller, Teresa, Bearth, Giulia, Herren, Gerhard, Wicker, Thomas, Keller, Beat, and University of Zurich

Subjects
UFSP13-7 Evolution in Action: From Genomes to Ecosystems, 10126 Department of Plant and Microbial Biology, 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center, General Agricultural and Biological Sciences, Education
Published
2022
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47. 454 sequencing put to the test using the complex genome of barley

Author

Wicker, Thomas, Schlagenhauf, Edith, Graner, Andreas, Close, Timothy J, Keller, Beat, and Stein, Nils

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Base Pairing, Base Sequence, Chromosomes, Artificial, Bacterial, Genes, Plant, Genome, Plant, Hordeum, Molecular Sequence Data, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundDuring the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing"), promising an approximately 100-fold increase in throughput over Sanger technology--an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley.ResultsTo study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC) clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences.ConclusionOur data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing and targeted sequence analysis can result in large regions of high-quality finished genomic sequences.

Published
2006

50. A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material

Author

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
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