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1. A catalogue of recombination coldspots in interspecific tomato hybrids.

Author

Fuentes, Roven Rommel, Nieuwenhuis, Ronald, Chouaref, Jihed, Hesselink, Thamara, van Dooijeweert, Willem, van den Broeck, Hetty C., Schijlen, Elio, Schouten, Henk J., Bai, Yuling, Fransz, Paul, Stam, Maike, de Jong, Hans, Trivino, Sara Diaz, de Ridder, Dick, van Dijk, Aalt D. J., and Peters, Sander A.

Subjects
TOMATOES, GENETIC variation, TOMATO breeding, GENETIC recombination, CULTIVATED plants, FOOD supply
Abstract

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties. Author summary: Ensuring a stable food supply in a changing climate hinges on enhancing plants' natural defenses and resilience. Breeders achieve this by crossing cultivated plants with their wild counterparts, mixing specific gene variants through genetic recombination. Yet, in some cases, certain genomic areas lack this recombination, particularly when crossing diverse plant types, limiting the mix of beneficial genes. In this study we used a method called pooled-pollen sequencing to map regions where genetic recombination does and doesn't occur when breeding tomatoes with five wild relatives. We discovered specific regions where genetic exchange is rare, mainly due to structural differences in DNA. These regions tend to be rich in repetitive DNA sequences and are less likely to swap genes during reproduction. Importantly, many of these "recombination coldspots" contain genes related to plant health and stress resistance, inadvertently limiting the effectiveness of breeding efforts. By identifying these regions, breeders can now make more informed choices when developing new tomato varieties, potentially by incorporating genes from other wild species to overcome these limitations and improve crop resilience. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Genome architecture and genetic diversity of allopolyploid okra (Abelmoschus esculentus).

Author

Nieuwenhuis, Ronald, Hesselink, Thamara, van den Broeck, Hetty C., Cordewener, Jan, Schijlen, Elio, Bakker, Linda, Diaz Trivino, Sara, Struss, Darush, de Hoop, Simon‐Jan, de Jong, Hans, and Peters, Sander A.

Subjects
*GENETIC variation, *OKRA, *GENOMES, *SINGLE nucleotide polymorphisms, *AMINO acid sequence, *EUCHROMATIN
Abstract

SUMMARY: The allopolyploid okra (Abelmoschus esculentus) unveiled telomeric repeats flanking distal gene‐rich regions and short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation. Ribosomal RNA (rRNA) genes organize into 5S clusters, distinct from the 18S–5.8S–28S units, indicating an S‐type rRNA gene arrangement. The assembly, in line with cytogenetic and cytometry observations, identifies 65 chromosomes and a 1.45 Gb genome size estimate in a haploid sibling. The lack of aberrant meiotic configurations implies limited to no recombination among sub‐genomes. k‐mer distribution analysis reveals 75% has a diploid nature and 15% heterozygosity. The configurations of Benchmarking Universal Single‐Copy Ortholog (BUSCO), k‐mer, and repeat clustering point to the presence of at least two sub‐genomes one with 30 and the other with 35 chromosomes, indicating the allopolyploid nature of the okra genome. Over 130 000 putative genes, derived from mapped IsoSeq data and transcriptome data from public okra accessions, exhibit a low genetic diversity of one single nucleotide polymorphisms per 2.1 kbp. The genes are predominantly located at the distal chromosome ends, declining toward central scaffold domains. Long terminal repeat retrotransposons prevail in central domains, consistent with the observed pericentromeric heterochromatin and distal euchromatin. Disparities in paralogous gene counts suggest potential sub‐genome differentiation implying possible sub‐genome dominance. Amino acid query sequences of putative genes facilitated phenol biosynthesis pathway annotation. Comparison with manually curated reference KEGG pathways from related Malvaceae species reveals the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra. Significance Statement: Our study delves into the genetic composition of allopolyploid okra and provides insight into the evolutionary dynamics of its sub‐genomes. Augmented by a comprehensive structural and functional genome annotation, our findings establish a robust foundation for advancing okra breeding practices. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids

Author

Fuentes, Roven Rommel, Nieuwenhuis, Ronald, Chouaref, Jihed, Hesselink, Thamara, van Dooijeweert, Willem, van den Broeck, Hetty C., Schijlen, Elio, Fransz, Paul, Stam, Maike, de Jong, Hans, Trivino, Sara Diaz, de Ridder, Dick, van Dijk, Aalt D.J., and Peters, Sander A.

Abstract

Tomato is the most consumed vegetable in the world. Increasing its natural resistance and resilience is key for ensuring food security within a changing climate. Plant breeders improve those traits by generating crosses of cultivated tomatoes with their wild relatives. Specific allele introgression relying on meiotic recombination, is hampered by structural divergence between parental genomes. However, previous studies of interspecific tomato hybridization focused in single cross or lacked resolution due to prohibitive sequencing costs of large segregating populations. Here, we used pooled-pollen sequencing to reveal unprecedented details of recombination patterns in five interspecific tomato hybrids. We detected hybrid-specific recombination coldspots that underscore the influence of structural divergence in shaping recombination landscape. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. We also found gene complexes associated with metabolic processes, stress resistance and domestication syndrome traits, revealing undesired consequences of recombination suppression to phenotypes. Finally, we demonstrate that by using resequencing data of wild and domesticated tomato populations, we can screen for alternative parental genomes to overcome recombination barriers. Overall, our results will allow breeders better informed decisions on generating disease-resistant and climate-resilient tomato.

Published
2022

7. Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids

Author

Fuentes, Roven Rommel, primary, Nieuwenhuis, Ronald, additional, Chouaref, Jihed, additional, Hesselink, Thamara, additional, van Dooijeweert, Willem, additional, van den Broeck, Hetty C, additional, Schijlen, Elio, additional, Fransz, Paul, additional, Stam, Maike, additional, de Jong, Hans, additional, Trivino, Sara Diaz, additional, de Ridder, Dick, additional, van Dijk, Aalt D. J., additional, and Peters, Sander A, additional

Published
2022
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16. Chasing breeding footprints through structural variations in Cucumis melo and wild relatives

Author

Demirci, Sevgin, Fuentes, Roven, van Dooijeweert, Willem, Aflitos, S.A., Schijlen, Elio, Hesselink, Thamara, de Ridder, Dick, van Dijk, Aalt-Jan, Peters, Sander, Demirci, Sevgin, Fuentes, Roven, van Dooijeweert, Willem, Aflitos, S.A., Schijlen, Elio, Hesselink, Thamara, de Ridder, Dick, van Dijk, Aalt-Jan, and Peters, Sander

Abstract

Cucumis melo (melon or muskmelon) is an important crop in the family of the Cucurbitaceae. Melon is cross pollinated and domesticated at several locations throughout the breeding history, resulting in highly diverse genetic structure in the germplasm. Yet, the relations among the groups and cultivars are still incomplete. We shed light on the melon breeding history, analysing structural variations (SV) ranging from 50 bp up to 100kb, identified from whole genome sequences of 100 selected melon accessions and wild relatives. Phylogenetic trees based on SV types completely resolve cultivars and wild accessions into two monophyletic groups and clustering of cultivars largely correlates with their geographic origin. Taking into account morphology, we found 6 mis-categorized cultivars. Unique inversions are more often shared between cultivars, carrying advantageous genes and do not directly originate from wild species. Approximately 60% of the inversion breaks carry a long poly A/T motif, and following observations in other plant species, suggest that inversions in melon likely resulted from meiotic recombination events. We show that the resistance genes in the linkage V region are expanded in the cultivar genomes compared to wild relatives. Furthermore, particular agronomic traits such as fruit ripening, fragrance and stress response are specifically selected for in the melon subspecies. These results represent distinctive footprints of selective breeding that shaped today’s melon. The sequences and genomic relations between land races, wild relatives and cultivars will serve the community to identify genetic diversity, optimize experimental designs, and enhance crop development.

Published
2020

19. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Yi, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Yang, Wencai, Huang, Sanwen, Du, Yongchen, Zhang, Zhonghua, Gao, Jianchang, Guo, Yanmei, Wang, Xiaoxuan, Li, Ying, He, Jun, Li, Chuanyou, Cheng, Zhukuan, Zuo, Jianru, Ren, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Wang, Bao, Li, Hongshuang, Li, Zhenjun, Fu, Fuyou, Chen, Bingtang, Han, Bin, Feng, Qi, Fan, Danlin, Wang, Ying, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, Richard McCombie, W., Lippman, Zachary B., Chia, Jer-Ming, Jiang, Ke, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Xu, Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigó, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Zhang, Junhong, Ye, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, James, Dixit, Rekha, Singh, Manju, Singh, Archana, Kumar Pal, Jitendra, Pandit, Awadhesh, Kumar Singh, Pradeep, Kumar Mahato, Ajay, Dogra, Vivek, Gaikwad, Kishor, Raj Sharma, Tilak, Mohapatra, Trilochan, Kumar Singh, Nagendra, Causse, Mathilde, Rothan, Christophe, Schiex, Thomas, Noirot, Céline, Bellec, Arnaud, Klopp, Christophe, Delalande, Corinne, Berges, Hélène, Mariette, Jérôme, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latché, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Pierre, Osorio, Sonia, Fernandez del Carmen, Asunción, Monforte, Antonio, Granell, Antonio, Fernandez-Muñoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Paolo, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Marco G. M., Feron, Richard M.C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Jo, Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Kim, Sangmi, Koo, Dal-Hoe, Lee, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Alain, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Jöcker, Anika, Warfsmann, Jens, Göbel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Elio G. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Jiang, Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Dong Kim, Byung, Park, Minkyu, Kim, Seungill, Yeom, Seon-In, Lee, Yong-Hwan, Choi, Yang-Do, Li, Guangcun, Gao, Jianwei, Liu, Yongsheng, Huang, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuñiga, Sheila, Wang, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Sandra, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Luis Goicoechea, Jose, Yu, Yeisoo, Kudrna, David, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Bala Gurazada, Aishwarya, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Sharma, Arun K., Khurana, Paramjit, Khurana, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Brad Barbazuk, W., Li, Jingping, Guo, Hui, Lee, Tae-Ho, Wang, Yupeng, Zhang, Dong, Paterson, Andrew H., Wang, Xiyin, Tang, Haibao, Barone, Amalia, Luisa Chiusano, Maria, Raffaella Ercolano, Maria, D’Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Fu, Ying, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Qu, Chunmei, Shi, Ruihua, White, Douglas, White, James, Xing, Yanbo, Yang, Keqin, Yi, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, Alessandro, D’Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Klein Lankhorst, René M., Beasley, Helen, McLaren, Karen, Nicholson, Christine, Riddle, Claire, and Gianese, Giulio

Published
2012
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20. Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing

Author

Rommel Fuentes, Roven, primary, Hesselink, Thamara, additional, Nieuwenhuis, Ronald, additional, Bakker, Linda, additional, Schijlen, Elio, additional, Dooijeweert, Willem, additional, Diaz Trivino, Sara, additional, Haan, Jorn R., additional, Sanchez Perez, Gabino, additional, Zhang, Xinyue, additional, Fransz, Paul, additional, Jong, Hans, additional, Dijk, Aalt D. J., additional, Ridder, Dick, additional, and Peters, Sander A., additional

Published
2020
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23. Additional file 16: of Correcting palindromes in long reads after whole-genome amplification

Author

Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De

Subjects
food and beverages
Abstract

The number of duplication or inversion events that were observed on contigs/scaffolds when aligned to human X-degenerate genes. (DOCX 26 kb)

Published
2018
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27. A 'footprint' of desiccation tolerance in the genome of Xerophyta viscosa

Author

Costa, Maria-Cecília D., Artur, Mariana A. S., Maia, Julio, Jonkheer, Eef, Derks, Martijn F. L., Nijveen, Harm, Williams, Brett, Mundree, Sagadevan G., Jiménez-Gómez, Jose M., Elio, Schijlen, Hesselink, Thamara, Schijlen, Elio G. W. M., Ligterink, Wilco, Oliver, Melvin J., Farrant, Jill M., Jill, Farrant, Henk, Hilhorst, and Hilhorst, Henk W. M.

Subjects
food and beverages
Abstract

Desiccation tolerance is common in seeds and various other organisms but only a few Angiosperm species possess vegetative desiccation tolerance. These 'resurrection species' may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration. Data revealed induction of transcripts typically associated with desiccation tolerance in seeds, and involvement of orthologues of ABI3 and ABI5, both key regulators of seed maturation. Dehydration resulted in both increased, but predominantly reduced transcript abundance of genomic 'clusters of desiccation-associated genes' (CoDAGs), reflecting the cessation of growth that allows for the expression of desiccation tolerance. Vegetative desiccation tolerance in X. viscosa was found to be uncoupled from drought-induced senescence. We provide strong support for the hypothesis that vegetative desiccation tolerance arose by redirection of genetic information from desiccation tolerant seeds.

Published
2017

28. Correcting palindromes in long reads after whole-genome amplification

Author

Warris, Sven, primary, Schijlen, Elio, additional, van de Geest, Henri, additional, Vegesna, Rahulsimham, additional, Hesselink, Thamara, additional, te Lintel Hekkert, Bas, additional, Sanchez Perez, Gabino, additional, Medvedev, Paul, additional, Makova, Kateryna D., additional, and de Ridder, Dick, additional

Published
2018
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29. A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Author

Costa, Maria Cecília D., Artur, Mariana A.S., Maia, Julio, Jonkheer, Eef, Derks, Martijn F.L., Nijveen, Harm, Williams, Brett, Mundree, Sagadevan G., Jiménez-Gómez, José M., Hesselink, Thamara, Schijlen, Elio G.W.M., Ligterink, Wilco, Oliver, Melvin J., Farrant, Jill M., Hilhorst, Henk W.M., Costa, Maria Cecília D., Artur, Mariana A.S., Maia, Julio, Jonkheer, Eef, Derks, Martijn F.L., Nijveen, Harm, Williams, Brett, Mundree, Sagadevan G., Jiménez-Gómez, José M., Hesselink, Thamara, Schijlen, Elio G.W.M., Ligterink, Wilco, Oliver, Melvin J., Farrant, Jill M., and Hilhorst, Henk W.M.

Published
2017

30. A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Author

Costa, Maria Cecilia, Artur, Mariana, Maia, Julio, Jonkheer, Eef, Derks, Martijn, Nijveen, Harm, Williams, Brett, Mundree, Sagadevan, Jimenez-Gomez, Jose, Hesselink, Thamara, Schijlen, Elio, Ligterink, Wilco, Oliver, Melvin, Farrant, Jill, Hilhorst, Henk, Costa, Maria Cecilia, Artur, Mariana, Maia, Julio, Jonkheer, Eef, Derks, Martijn, Nijveen, Harm, Williams, Brett, Mundree, Sagadevan, Jimenez-Gomez, Jose, Hesselink, Thamara, Schijlen, Elio, Ligterink, Wilco, Oliver, Melvin, Farrant, Jill, and Hilhorst, Henk

Abstract

Desiccation tolerance is common in seeds and various other organisms but only a few Angiosperm species possess vegetative desiccation tolerance. These ‘resurrection species’ may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration. Data revealed induction of transcripts typically associated with desiccation tolerance in seeds, and involvement of orthologues of ABI3 and ABI5, both key regulators of seed maturation. Dehydration resulted in both increased, but predominantly reduced transcript abundance of genomic ‘clusters of desiccation-associated genes’ (CoDAGs), reflecting the cessation of growth that allows for the expression of desiccation tolerance. Vegetative desiccation tolerance in X. viscosa was found to be uncoupled from drought-induced senescence. We provide strong support for the hypothesis that vegetative desiccation tolerance arose by redirection of genetic information from desiccation tolerant seeds.

Published
2017

31. Correcting palindromes in long reads after whole-genome amplification

Author

Warris, Sven, primary, Schijlen, Elio, additional, van de Geest, Henri, additional, Vegesna, Rahulsimham, additional, Hesselink, Thamara, additional, te Lintel Hekkert, Bas, additional, Sanchez Perez, Gabino, additional, Medvedev, Paul, additional, Makova, Kateryna D., additional, and de Ridder, Dick, additional

Published
2017
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32. A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Author

Costa, Maria-Cecília D., primary, Artur, Mariana A. S., additional, Maia, Julio, additional, Jonkheer, Eef, additional, Derks, Martijn F. L., additional, Nijveen, Harm, additional, Williams, Brett, additional, Mundree, Sagadevan G., additional, Jiménez-Gómez, José M., additional, Hesselink, Thamara, additional, Schijlen, Elio G. W. M., additional, Ligterink, Wilco, additional, Oliver, Melvin J., additional, Farrant, Jill M., additional, and Hilhorst, Henk W. M., additional

Published
2017
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36. Synteny in Toxigenic FusariumSpecies: The Fumonisin Gene Cluster and the Mating Type Region as Examples

Author

Waalwijk, Cees, van der Lee, Theo, de Vries, Ineke, Hesselink, Thamara, Arts, Joop, and Kema, Gert

Abstract

A comparative genomic approach was used to study the mating type locus and the gene cluster involved in toxin production (fumonisin) in Fusarium proliferatum, a pathogen with a wide host range and a complex toxin profile. A BAC library, generated from F. proliferatumisolate ITEM 2287, was used to identify chromosomal regions flanking the mating type locus and the gene cluster involved in the biosynthesis of fumonisin. These regions were sequenced and compared with corresponding sequences in other ascomycetes. The results demonstrated that the level of synteny between ascomycetes can vary greatly for different genomic regions and that the level of similarity of genes within a region can also fluctuate strongly. Synteny was found in the regions flanking the mating type idiomorph among ascomycetes that supposedly diverged 280 million years ago. The fumonisin gene clusters of F. proliferatumand F. verticillioideswere completely syntenic but absent in F. graminearum. The regions flanking the fumonisin gene clusters were highly dissimilar between F. proliferatumand F. verticillioides, whereas they formed a continuous region in F. graminearum.This indicates that the fumonisin gene cluster has been inserted at different genome locations in both species. Surprisingly low similarity was found between the corresponding genes within the fumonisin cluster of F. proliferatumand F. verticillioides, compared to other genomic sequences indicative for two independent acquisition events from distinct genetic sources. The results demonstrate the power of comparative genomics for gene annotation and for studies on the evolution of genes, gene-clusters and species.

Published
2004
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37. Major Changes in Fusariumspp. in Wheat in the Netherlands

Author

Waalwijk, Cees, Kastelein, Pieter, de Vries, Ineke, Kerényi, Zoltan, van der Lee, Theo, Hesselink, Thamara, Köhl, Jürgen, and Kema, Gert

Abstract

The re-emergence of fusarium head blight throughout the world and especially in Western Europe prompted a survey of the situation in the Netherlands. To allow for a high throughput screening of large numbers of samples, a diagnostic PCR method was developed to detect the most common species of Fusariumoccurring on wheat. Seven primer pairs were tested for their ability to identify isolates of Fusarium avenaceum, F. culmorum, F. graminearum, F. poae, F. proliferatumand Microdochium nivalevar. majusand M. nivalevar. nivale. Each primer pair only generated a PCR product with the corresponding Fusariumspecies and all PCR fragments had different molecular sizes. This allowed the generation of these amplicons using a mixture of all seven primer pairs. The robustness of this multiplex PCR encouraged us to screen a large series of isolates collected in 2000 and 2001. In both years 40 fields were sampled leading to a collection of 209 isolates from 2000 and 145 isolates from 2001. The results of the multiplex PCR demonstrated that F. graminearumwas the most abundant species in the Fusariumcomplex on wheat in both years. This is in sharp contrast to reports from the 1980s and early 1990s, which found F. culmorumas the predominant species. Primers derived from the tri7and tri13genes, which are implicated in the acetylation and oxygenation of the C-4 atom of the backbone of the trichothecene molecule, were used to discriminate between deoxynivalenol and nivalenol (NIV) producers. The populations of F. culmorumand F. graminearumboth showed a slight increase in NIV-producers in 2001.

Published
2003
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42. Chasing breeding footprints through structural variations in Cucumis melo and wild relatives.

Author

Demirci, Sevgin, Fuentes, Roven Rommel, Dooijeweert, Willem van, Aflitos, Saulo, Schijlen, Elio, Hesselink, Thamara, Ridder, Dick de, van Dijk, Aalt D. J., and Peters, Sander

Subjects
*MUSKMELON, *CHROMOSOME inversions, *GENETIC variation, *WATERMELONS, *FRUIT ripening, *CROP development, *PLANT species
Abstract

Cucumis melo (melon or muskmelon) is an important crop in the family of the Cucurbitaceae. Melon is cross pollinated and domesticated at several locations throughout the breeding history, resulting in highly diverse genetic structure in the germplasm. Yet, the relations among the groups and cultivars are still incomplete. We shed light on the melonbreeding history, analyzing structural variations ranging from 50 bp up to 100 kb, identified from whole genome sequences of 100 selected melon accessions and wild relatives. Phylogenetic trees based on SV types completely resolve cultivars and wild accessions into two monophyletic groups and clustering of cultivars largely correlates with their geographic origin. Taking into account morphology, we found six mis-categorized cultivars. Unique inversions are more often shared between cultivars, carrying advantageous genes and do not directly originate from wild species. Approximately 60% of the inversion breaks carry a long poly A/T motif, and following observations in other plant species, suggest that inversions in melon likely resulted from meiotic recombination events. We show that resistance genes in the linkage V region are expanded in the cultivar genomes compared to wild relatives. Furthermore, particular agronomic traits such as fruit ripening, fragrance, and stress response are specifically selected for in the melon subspecies. These results represent distinctive footprints of selective breeding that shaped today’s melon. The sequences and genomic relations between land races, wild relatives, and cultivars will serve the community to identify genetic diversity, optimize experimental designs, and enhance crop development. [ABSTRACT FROM AUTHOR]

Published
2021
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