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Xiong W, van Workum DJM, Berke L, Bakker LV, Schijlen E, Becker FFM, van de Geest H, Peters S, Michelmore R, van Treuren R, Jeuken M, Smit S, Schranz ME. Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding. G3 (Bethesda) 2023; 13:jkad204. [PMID: 37740775 PMCID: PMC10627274 DOI: 10.1093/g3journal/jkad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 09/25/2023]
Abstract
Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x = 2n = 18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicated the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Dirk-Jan M van Workum
- Bioinformatics Group, Wageningen University & Research, P.O. Box 633, Wageningen, 6700 AP, The Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Linda V Bakker
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Elio Schijlen
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Frank F M Becker
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
- Laboratory of Genetics, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Henri van de Geest
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Sander Peters
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Richard Michelmore
- The Genome Center, Genome & Biomedical Sciences Facility, University of California, Davis, 451 East Health Sciences Drive, Davis, CA 95616-8816, USA
| | - Rob van Treuren
- Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Marieke Jeuken
- Plant Breeding Group, Wageningen University & Research, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University & Research, P.O. Box 633, Wageningen, 6700 AP, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
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2
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Xiong W, Risse J, Berke L, Zhao T, van de Geest H, Oplaat C, Busscher M, Ferreira de Carvalho J, van der Meer IM, Verhoeven KJF, Schranz ME, Vijverberg K. Phylogenomic analysis provides insights into MADS-box and TCP gene diversification and floral development of the Asteraceae, supported by de novo genome and transcriptome sequences from dandelion ( Taraxacum officinale). Front Plant Sci 2023; 14:1198909. [PMCID: PMC10338227 DOI: 10.3389/fpls.2023.1198909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023]
Abstract
The Asteraceae is the largest angiosperm family with more than 25,000 species. Individual studies have shown that MADS-box and TCP transcription factors are regulators of the development and symmetry of flowers, contributing to their iconic flower-head (capitulum) and floret. However, a systematic study of MADS-box and TCP genes across the Asteraceae is lacking. We performed a comparative analysis of genome sequences of 33 angiosperm species including our de novo assembly of diploid sexual dandelion (Taraxacum officinale) and 11 other Asteraceae to investigate the lineage-specific evolution of MADS-box and TCP genes in the Asteraceae. We compared the phylogenomic results of MADS-box and TCP genes with their expression in T. officinale floral tissues at different developmental stages to demonstrate the regulation of genes with Asteraceae-specific attributes. Here, we show that MADS-box MIKCc and TCP-CYCLOIDEA (CYC) genes have expanded in the Asteraceae. The phylogenomic analysis identified AGAMOUS-like (AG-like: SEEDSTICK [STK]-like), SEPALATA-like (SEP3-like), and TCP-PROLIFERATING CELL FACTOR (PCF)-like copies with lineage-specific genomic contexts in the Asteraceae, Cichorioideae, or dandelion. Different expression patterns of some of these gene copies suggest functional divergence. We also confirm the presence and revisit the evolutionary history of previously named “Asteraceae-Specific MADS-box genes (AS-MADS).” Specifically, we identify non-Asteraceae homologs, indicating a more ancient origin of this gene clade. Syntenic relationships support that AS-MADS is paralogous to FLOWERING LOCUS C (FLC) as demonstrated by the shared ancient duplication of FLC and SEP3.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Judith Risse
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Tao Zhao
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | | | - Carla Oplaat
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Marco Busscher
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
- Bioscience, Wageningen University and Research, Wageningen, Netherlands
| | - Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Kitty Vijverberg
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
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Warris S, Schijlen E, van de Geest H, Vegesna R, Hesselink T, Te Lintel Hekkert B, Sanchez Perez G, Medvedev P, Makova KD, de Ridder D. Correcting palindromes in long reads after whole-genome amplification. BMC Genomics 2018; 19:798. [PMID: 30400848 PMCID: PMC6218980 DOI: 10.1186/s12864-018-5164-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/15/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long sequencing reads. RESULTS Here, we present Pacasus, a tool for correcting such errors. Two datasets show that it markedly improves read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. CONCLUSIONS With Pacasus long-read technologies become available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.
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Affiliation(s)
- Sven Warris
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.
| | - Elio Schijlen
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.,Present address Genetwister Technologies BV, Wageningen, The Netherlands
| | - Rahulsimham Vegesna
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Computation, Bioinformatics, Statistics Graduate Training Program, Pennsylvania State University, University Park, State College, PA, 16802, USA.,The Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thamara Hesselink
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Bas Te Lintel Hekkert
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.,Present address Genetwister Technologies BV, Wageningen, The Netherlands
| | - Paul Medvedev
- The Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Computer Science and Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.,The Center for Medical Genomics, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Kateryna D Makova
- The Center for Medical Genomics, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
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Warris S, Timal NRN, Kempenaar M, Poortinga AM, van de Geest H, Varbanescu AL, Nap JP. pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment. PLoS One 2018; 13:e0190279. [PMID: 29293576 PMCID: PMC5749749 DOI: 10.1371/journal.pone.0190279] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 12/11/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. RESULTS The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. CONCLUSIONS pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.
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Affiliation(s)
- Sven Warris
- Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences Groningen, Groningen, the Netherlands.,Applied Bioinformatics, Wageningen University and Research, Wageningen, the Netherlands
| | - N Roshan N Timal
- Parallel and Distributed Systems, Delft University of Technology, Delft, the Netherlands
| | - Marcel Kempenaar
- Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences Groningen, Groningen, the Netherlands
| | - Arne M Poortinga
- Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences Groningen, Groningen, the Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Wageningen University and Research, Wageningen, the Netherlands
| | - Ana L Varbanescu
- Parallel and Distributed Systems, Delft University of Technology, Delft, the Netherlands
| | - Jan-Peter Nap
- Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences Groningen, Groningen, the Netherlands.,Applied Bioinformatics, Wageningen University and Research, Wageningen, the Netherlands
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5
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Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B. De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing. Plant Cell 2017; 29:2336-2348. [PMID: 29025960 PMCID: PMC5774570 DOI: 10.1105/tpc.17.00521] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/15/2017] [Accepted: 10/11/2017] [Indexed: 05/19/2023]
Abstract
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
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Affiliation(s)
- Maximilian H-W Schmidt
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Alexander Vogel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Alisandra K Denton
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Benjamin Istace
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope, 91057 Evry, France
| | - Alexandra Wormit
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | | | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Janina Maß
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Christian Pfaff
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Ulrich Schurr
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Roger Chetelat
- C.M. Rick Tomato Genetics Resource Center, Department of Plant Sciences, University of California, Davis, California 95616
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope, 91057 Evry, France
| | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dani Zamir
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Anthony M Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
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Schulze S, Urzica E, Reijnders MJMF, van de Geest H, Warris S, Bakker LV, Fufezan C, Martins Dos Santos VAP, Schaap PJ, Peters SA, Hippler M. Identification of methylated GnTI-dependent N-glycans in Botryococcus brauni. New Phytol 2017; 215:1361-1369. [PMID: 28737213 DOI: 10.1111/nph.14713] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/15/2017] [Indexed: 05/21/2023]
Abstract
In contrast to mammals and vascular plants, microalgae show a high diversity in the N-glycan structures of complex N-glycoproteins. Although homologues for β1,2-N-acetylglucosaminyltransferase I (GnTI), a key enzyme in the formation of complex N-glycans, have been identified in several algal species, GnTI-dependent N-glycans have not been detected so far. We have performed an N-glycoproteomic analysis of the hydrocarbon oils accumulating green microalgae Botryococcus braunii. Thereby, the analysis of intact N-glycopeptides allowed the determination of N-glycan compositions. Furthermore, insights into the role of N-glycosylation in B. braunii were gained from functional annotation of the identified N-glycoproteins. In total, 517 unique N-glycosylated peptides have been identified, including intact N-glycopeptides that harbored N-acetylhexosamine (HexNAc) at the nonreducing end. Surprisingly, these GnTI-dependent N-glycans were also found to be modified with (di)methylated hexose. The identification of GnTI-dependent N-glycans in combination with N-glycan methylation in B. braunii revealed an uncommon type of N-glycan processing in this microalgae.
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Affiliation(s)
- Stefan Schulze
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, 48143, Germany
| | - Eugen Urzica
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, 48143, Germany
| | - Maarten J M F Reijnders
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, 6703 HB, the Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Wageningen University and Research Centre, Wageningen, 6708 PB, the Netherlands
| | - Sven Warris
- Applied Bioinformatics, Wageningen University and Research Centre, Wageningen, 6708 PB, the Netherlands
| | - Linda V Bakker
- Applied Bioinformatics, Wageningen University and Research Centre, Wageningen, 6708 PB, the Netherlands
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, 48143, Germany
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, 6703 HB, the Netherlands
- LifeGlimmer GmbH, Berlin, 12163, Germany
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, 6703 HB, the Netherlands
| | - Sander A Peters
- Applied Bioinformatics, Wageningen University and Research Centre, Wageningen, 6708 PB, the Netherlands
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, 48143, Germany
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7
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Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, De Saeger S, Haesaert G, Waalwijk C, van der Lee T. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genomics 2016; 17:670. [PMID: 27552804 PMCID: PMC4994206 DOI: 10.1186/s12864-016-2941-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/14/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. RESULTS Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. CONCLUSIONS For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
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Affiliation(s)
- Adriaan Vanheule
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Wageningen UR, Wageningen, The Netherlands
| | - Kris Audenaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sarah De Saeger
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Geert Haesaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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8
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Kooke R, Kruijer W, Bours R, Becker F, Kuhn A, van de Geest H, Buntjer J, Doeswijk T, Guerra J, Bouwmeester H, Vreugdenhil D, Keurentjes JJB. Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis. Plant Physiol 2016; 170:2187-203. [PMID: 26869705 PMCID: PMC4825126 DOI: 10.1104/pp.15.00997] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 02/11/2016] [Indexed: 05/05/2023]
Abstract
Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.
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Affiliation(s)
- Rik Kooke
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Willem Kruijer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Ralph Bours
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Frank Becker
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - André Kuhn
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Henri van de Geest
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Jaap Buntjer
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Timo Doeswijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - José Guerra
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Dick Vreugdenhil
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
| | - Joost J B Keurentjes
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
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9
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Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L, Bakker F, Dirks R, Breit T, Gravendeel B, Huits H, Struss D, Swanson-Wagner R, van Leeuwen H, van Ham RCHJ, Fito L, Guignier L, Sevilla M, Ellul P, Ganko E, Kapur A, Reclus E, de Geus B, van de Geest H, Te Lintel Hekkert B, van Haarst J, Smits L, Koops A, Sanchez-Perez G, van Heusden AW, Visser R, Quan Z, Min J, Liao L, Wang X, Wang G, Yue Z, Yang X, Xu N, Schranz E, Smets E, Vos R, Rauwerda J, Ursem R, Schuit C, Kerns M, van den Berg J, Vriezen W, Janssen A, Datema E, Jahrman T, Moquet F, Bonnet J, Peters S. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 2014; 80:136-48. [PMID: 25039268 DOI: 10.1111/tpj.12616] [Citation(s) in RCA: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 05/20/2023]
Abstract
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
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Folta A, Severing EI, Krauskopf J, van de Geest H, Verver J, Nap JP, Mlynarova L. Over-expression of Arabidopsis AtCHR23 chromatin remodeling ATPase results in increased variability of growth and gene expression. BMC Plant Biol 2014; 14:76. [PMID: 24666886 PMCID: PMC3987066 DOI: 10.1186/1471-2229-14-76] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/17/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND Plants are sessile organisms that deal with their -sometimes adverse- environment in well-regulated ways. Chromatin remodeling involving SWI/SNF2-type ATPases is thought to be an important epigenetic mechanism for the regulation of gene expression in different developmental programs and for integrating these programs with the response to environmental signals. In this study, we report on the role of chromatin remodeling in Arabidopsis with respect to the variability of growth and gene expression in relationship to environmental conditions. RESULTS Already modest (2-fold) over-expression of the AtCHR23 ATPase gene in Arabidopsis results in overall reduced growth compared to the wild-type. Detailed analyses show that in the root, the reduction of growth is due to reduced cell elongation. The reduced-growth phenotype requires sufficient light and is magnified by applying deliberate abiotic (salt, osmotic) stress. In contrast, the knockout mutation of AtCHR23 does not lead to such visible phenotypic effects. In addition, we show that over-expression of AtCHR23 increases the variability of growth in populations of genetically identical plants. These data indicate that accurate and controlled expression of AtCHR23 contributes to the stability or robustness of growth. Detailed RNAseq analyses demonstrate that upon AtCHR23 over-expression also the variation of gene expression is increased in a subset of genes that associate with environmental stress. The larger variation of gene expression is confirmed in individual plants with the help of independent qRT-PCR analysis. CONCLUSIONS Over-expression of AtCHR23 gives Arabidopsis a phenotype that is markedly different from the growth arrest phenotype observed upon over-expression of AtCHR12, the paralog of AtCHR23, in response to abiotic stress. This demonstrates functional sub-specialization of highly similar ATPases in Arabidopsis. Over-expression of AtCHR23 increases the variability of growth among genetically identical individuals in a way that is consistent with increased variability of expression of a distinct subset of genes that associate with environmental stress. We propose that ATCHR23-mediated chromatin remodeling is a potential component of a buffer system in plants that protects against environmentally-induced phenotypic and transcriptional variation.
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Affiliation(s)
- Adam Folta
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Edouard I Severing
- Laboratory of Genetics, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Julian Krauskopf
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- Present address: Department of Toxigenomics, Maastricht University, Maastricht, The Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Jan Verver
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Jan-Peter Nap
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Ludmila Mlynarova
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
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11
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Tikunov YM, Molthoff J, de Vos RC, Beekwilder J, van Houwelingen A, van der Hooft JJ, Nijenhuis-de Vries M, Labrie CW, Verkerke W, van de Geest H, Viquez Zamora M, Presa S, Rambla JL, Granell A, Hall RD, Bovy AG. Non-smoky glycosyltransferase1 prevents the release of smoky aroma from tomato fruit. Plant Cell 2013; 25:3067-78. [PMID: 23956261 PMCID: PMC3784599 DOI: 10.1105/tpc.113.114231] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/15/2013] [Accepted: 08/01/2013] [Indexed: 05/18/2023]
Abstract
Phenylpropanoid volatiles are responsible for the key tomato fruit (Solanum lycopersicum) aroma attribute termed "smoky." Release of these volatiles from their glycosylated precursors, rather than their biosynthesis, is the major determinant of smoky aroma in cultivated tomato. using a combinatorial omics approach, we identified the non-smoky glycosyltransferase1 (NSGT1) gene. Expression of NSGT1 is induced during fruit ripening, and the encoded enzyme converts the cleavable diglycosides of the smoky-related phenylpropanoid volatiles into noncleavable triglycosides, thereby preventing their deglycosylation and release from tomato fruit upon tissue disruption. In an nsgt1/nsgt1 background, further glycosylation of phenylpropanoid volatile diglycosides does not occur, thereby enabling their cleavage and the release of corresponding volatiles. Using reverse genetics approaches, the NSGT1-mediated glycosylation was shown to be the molecular mechanism underlying the major quantitative trait locus for smoky aroma. Sensory trials with transgenic fruits, in which the inactive nsgt1 was complemented with the functional NSGT1, showed a significant and perceivable reduction in smoky aroma. NSGT1 may be used in a precision breeding strategy toward development of tomato fruits with distinct flavor phenotypes.
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Affiliation(s)
- Yury M. Tikunov
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
- Address correspondence to
| | - Jos Molthoff
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
| | - Ric C.H. de Vos
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
- Netherlands Metabolomics Centre, 2333 CC Leiden, The Netherlands
| | - Jules Beekwilder
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
| | | | | | | | | | - Wouter Verkerke
- Wageningen UR Glastuinbouw, 2665 MV Bleiswijk, The Netherlands
| | - Henri van de Geest
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
| | | | - Silvia Presa
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Jose Luis Rambla
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Robert D. Hall
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
- Netherlands Metabolomics Centre, 2333 CC Leiden, The Netherlands
| | - Arnaud G. Bovy
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Centre for Biosystems Genomics, 6700 PB Wageningen, The Netherlands
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D’Agostino N, Golas T, van de Geest H, Bombarely A, Dawood T, Zethof J, Driedonks N, Wijnker E, Bargsten J, Nap JP, Mariani C, Rieu I. Genomic analysis of the native European Solanum species, S. dulcamara. BMC Genomics 2013; 14:356. [PMID: 23713999 PMCID: PMC3680029 DOI: 10.1186/1471-2164-14-356] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been recognized as one of the alternative hosts for pathogens and pests responsible for many important diseases in potato, such as Phytophthora. At the same time, it may represent an alternative source of resistance genes against these diseases. Despite its unique ecology and potential as a genetic resource, genomic research tools are lacking for S. dulcamara. We have taken advantage of next-generation sequencing to speed up research on and use of this non-model species. RESULTS In this work, we present the first large-scale characterization of the S. dulcamara transcriptome. Through comparison of RNAseq reads from two different accessions, we were able to predict transcript-based SNP and SSR markers. Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated. Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements. This allowed a better estimation of the evolutionary moment of rearrangements in a number of cases and showed that chromosomal breakpoints are regularly re-used. CONCLUSION Knowledge and tools developed as part of this study pave the way for future genomic research and exploitation of this wild Solanum species. The transcriptome assembly represents a resource for functional analysis of genes underlying interesting biological and agronomical traits and, in the absence of the full genome, provides a reference for RNAseq gene expression profiling aimed at understanding the unique biology of S. dulcamara. Cross-species orthology-based marker selection is shown to be a powerful tool to quickly generate a comparative genetic map, which may speed up gene mapping and contribute to the understanding of genome evolution within the Solanaceae family.
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Affiliation(s)
- Nunzio D’Agostino
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
- Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di ricerca per l’orticoltura, via Cavalleggeri 25, Pontecagnano, SA, 84098, Italy
| | - Tomek Golas
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University & Research Centre, PO Box 619, Wageningen, 6700 AP, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Aureliano Bombarely
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York, 14853-1801, USA
| | - Thikra Dawood
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Jan Zethof
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Nicky Driedonks
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Joachim Bargsten
- Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University & Research Centre, PO Box 619, Wageningen, 6700 AP, The Netherlands
| | - Jan-Peter Nap
- Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University & Research Centre, PO Box 619, Wageningen, 6700 AP, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Celestina Mariani
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Ivo Rieu
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
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13
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Víquez-Zamora M, Vosman B, van de Geest H, Bovy A, Visser RGF, Finkers R, van Heusden AW. Tomato breeding in the genomics era: insights from a SNP array. BMC Genomics 2013; 14:354. [PMID: 23711327 PMCID: PMC3680325 DOI: 10.1186/1471-2164-14-354] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/20/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. RESULTS From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum 'Moneymaker' from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoes earlier results. CONCLUSIONS Our results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome.
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Affiliation(s)
- Marcela Víquez-Zamora
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen Campus, PB Wageningen, 6807, The Netherlands
| | - Ben Vosman
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Henri van de Geest
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
- Bioscience, Plant Research International, P.O. Box 619, AP Wageningen, 6700, The Netherlands
| | - Arnaud Bovy
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Richard GF Visser
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Richard Finkers
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Adriaan W van Heusden
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
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Karlova R, van Haarst JC, Maliepaard C, van de Geest H, Bovy AG, Lammers M, Angenent GC, de Maagd RA. Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot 2013; 64:1863-78. [PMID: 23487304 PMCID: PMC3638818 DOI: 10.1093/jxb/ert049] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) play important roles in plant development through regulation of gene expression by mRNA degradation or translational inhibition. Despite the fact that tomato (Solanum lycopersicum) is the model system for studying fleshy fruit development and ripening, only a few experimentally proven miRNA targets are known, and the role of miRNA action in these processes remains largely unknown. Here, by using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development, a total of 119 target genes of miRNAs were identified. Of these, 106 appeared to be new targets. A large part of the identified targets (56) coded for transcription factors. Auxin response factors, as well as two known ripening regulators, colorless non-ripening (CNR) and APETALA2a (SlAP2a), with developmentally regulated degradation patterns were identified. The levels of the intact messenger of both CNR and AP2a are actively modulated during ripening, by miR156/157 and miR172, respectively. Additionally, two TAS3-mRNA loci were identified as targets of miR390. Other targets such as Argonaute 1 (AGO1), shown to be involved in miRNA biogenesis in other plant species, were identified, which suggests a feedback loop regulation of this process. In this study, it is shown that miRNA-guided cleavage of mRNAs is likely to play an important role in tomato fruit development and ripening.
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Affiliation(s)
- Rumyana Karlova
- Laboratory of Molecular Biology, Wageningen University, 6700 ET Wageningen, The Netherlands
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- *Present address: Department of Molecular Plant Physiology, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Jan C. van Haarst
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), 6700 AB Wageningen, The Netherlands
| | - Chris Maliepaard
- Business Unit Biodiversity and Breeding, Plant Research International, 6700 AP Wageningen, The Netherlands
| | - Henri van de Geest
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), 6700 AB Wageningen, The Netherlands
| | - Arnaud G. Bovy
- Business Unit Biodiversity and Breeding, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), 6700 AB Wageningen, The Netherlands
| | - Michiel Lammers
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), 6700 AB Wageningen, The Netherlands
| | - Gerco C. Angenent
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), 6700 AB Wageningen, The Netherlands
| | - Ruud A. de Maagd
- Business Unit Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), 6700 AB Wageningen, The Netherlands
- †To whom correspondence should be addressed. E-mail:
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