1
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Beier S, Ulpinnis C, Schwalbe M, Münch T, Hoffie R, Koeppel I, Hertig C, Budhagatapalli N, Hiekel S, Pathi KM, Hensel G, Grosse M, Chamas S, Gerasimova S, Kumlehn J, Scholz U, Schmutzer T. Kmasker plants - a tool for assessing complex sequence space in plant species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:631-642. [PMID: 31823436 DOI: 10.1111/tpj.14645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Many plant genomes display high levels of repetitive sequences. The assembly of these complex genomes using short high-throughput sequence reads is still a challenging task. Underestimation or disregard of repeat complexity in these datasets can easily misguide downstream analysis. Detection of repetitive regions by k-mer counting methods has proved to be reliable. Easy-to-use applications utilizing k-mer counting are in high demand, especially in the domain of plants. We present Kmasker plants, a tool that uses k-mer count information as an assistant throughout the analytical workflow of genome data that is provided as a command-line and web-based solution. Beside its core competence to screen and mask repetitive sequences, we have integrated features that enable comparative studies between different cultivars or closely related species and methods that estimate target specificity of guide RNAs for application of site-directed mutagenesis using Cas9 endonuclease. In addition, we have set up a web service for Kmasker plants that maintains pre-computed indices for 10 of the economically most important cultivated plants. Source code for Kmasker plants has been made publically available at https://github.com/tschmutzer/kmasker. The web service is accessible at https://kmasker.ipk-gatersleben.de.
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Chris Ulpinnis
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, 06120, Halle, Germany
| | - Markus Schwalbe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Thomas Münch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Robert Hoffie
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Iris Koeppel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Christian Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Nagaveni Budhagatapalli
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Stefan Hiekel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Krishna M Pathi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Martin Grosse
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Sindy Chamas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Sophia Gerasimova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Thomas Schmutzer
- Department of Natural Sciences III, Institute for Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
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2
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Himmelbach A, Ruban A, Walde I, Šimková H, Doležel J, Hastie A, Stein N, Mascher M. Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1309-1316. [PMID: 30256471 DOI: 10.1111/tpj.14109] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 09/14/2018] [Indexed: 05/02/2023]
Abstract
Chromosomal inversions occur in natural populations of many species, and may underlie reproductive isolation and local adaptation. Traditional methods of inversion discovery are labor-intensive and lack sensitivity. Here, we report the use of three-dimensional contact probabilities between genomic loci as assayed by chromosome-conformation capture sequencing (Hi-C) to detect multi-megabase polymorphic inversions in four barley genotypes. Inversions are validated by fluorescence in situ hybridization and Bionano optical mapping. We propose Hi-C as a generally applicable method for inversion discovery in natural populations.
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Affiliation(s)
- Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Ines Walde
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Alex Hastie
- BioNano Genomics Inc., 9640 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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3
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Marques A, Klemme S, Houben A. Evolution of Plant B Chromosome Enriched Sequences. Genes (Basel) 2018; 9:genes9100515. [PMID: 30360448 PMCID: PMC6210368 DOI: 10.3390/genes9100515] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/13/2018] [Accepted: 10/18/2018] [Indexed: 01/10/2023] Open
Abstract
B chromosomes are supernumerary chromosomes found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several distinct types of repeated DNA elements. Although the evolution of B chromosomes has been the subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences are not fully understood. Recently, new genomic approaches have shed light on the origin and accumulation of different classes of repetitive sequences in the process of B chromosome formation and evolution. Here we discuss the impact of repetitive sequences accumulation on the evolution of plant B chromosomes.
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Affiliation(s)
- André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Av. Manoel Severino Barbosa, 57309-005 Arapiraca-AL, Brazil.
| | - Sonja Klemme
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
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4
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Ruban A, Schmutzer T, Scholz U, Houben A. How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes. Genes (Basel) 2017; 8:E294. [PMID: 29068386 PMCID: PMC5704207 DOI: 10.3390/genes8110294] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
Accessory, supernumerary, or-most simply-B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS), their structure comprises fragments of standard (A) chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.
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Affiliation(s)
- Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany.
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5
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From plant genomes to phenotypes. J Biotechnol 2017; 261:46-52. [PMID: 28602791 DOI: 10.1016/j.jbiotec.2017.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/27/2017] [Accepted: 06/07/2017] [Indexed: 12/21/2022]
Abstract
Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis. Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.
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6
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Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön CC, Scholz U. Towards a whole-genome sequence for rye (Secale cereale L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:853-869. [PMID: 27888547 DOI: 10.1111/tpj.13436] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 05/18/2023]
Abstract
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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Affiliation(s)
- Eva Bauer
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Ivan Barilar
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mihaela M Martis
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Bernd Hackauf
- Julius Kühn-Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Andres Gordillo
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Peer Wilde
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Malthe Schmidt
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Karl Schmid
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
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7
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Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer KFX, Platzer M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1511-22. [PMID: 26801048 PMCID: PMC5066668 DOI: 10.1111/pbi.12511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
Abstract
Hierarchical shotgun sequencing remains the method of choice for assembling high-quality reference sequences of complex plant genomes. The efficient exploitation of current high-throughput technologies and powerful computational facilities for large-insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole-genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high-quality assemblies of a large number of clones to assemble map-based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Klaus F X Mayer
- Plant Genome and System Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
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8
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Spannagl M, Alaux M, Lange M, Bolser DM, Bader KC, Letellier T, Kimmel E, Flores R, Pommier C, Kerhornou A, Walts B, Nussbaumer T, Grabmuller C, Chen J, Colmsee C, Beier S, Mascher M, Schmutzer T, Arend D, Thanki A, Ramirez-Gonzalez R, Ayling M, Ayling S, Caccamo M, Mayer KFX, Scholz U, Steinbach D, Quesneville H, Kersey PJ. transPLANT Resources for Triticeae Genomic Data. THE PLANT GENOME 2016; 9. [PMID: 27898761 DOI: 10.3835/plantgenome2015.06.0038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The genome sequences of many important Triticeae species, including bread wheat ( L.) and barley ( L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT () is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.
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9
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Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosome Res 2016; 24:231-42. [DOI: 10.1007/s10577-016-9518-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/31/2016] [Accepted: 02/01/2016] [Indexed: 01/05/2023]
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10
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Schmutzer T, Samans B, Dyrszka E, Ulpinnis C, Weise S, Stengel D, Colmsee C, Lespinasse D, Micic Z, Abel S, Duchscherer P, Breuer F, Abbadi A, Leckband G, Snowdon R, Scholz U. Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus. Sci Data 2015; 2:150072. [PMID: 26647166 PMCID: PMC4672681 DOI: 10.1038/sdata.2015.72] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/02/2015] [Indexed: 11/09/2022] Open
Abstract
Brassica napus (oilseed rape, canola) is one of the world's most important sources of vegetable oil for human nutrition and biofuel, and also a model species for studies investigating the evolutionary consequences of polyploidisation. Strong bottlenecks during its recent origin from interspecific hybridisation, and subsequently through intensive artificial selection, have severely depleted the genetic diversity available for breeding. On the other hand, high-throughput genome profiling technologies today provide unprecedented scope to identify, characterise and utilise genetic diversity in primary and secondary crop gene pools. Such methods also enable implementation of genomic selection strategies to accelerate breeding progress. The key prerequisite is availability of high-quality sequence data and identification of high-quality, genome-wide sequence polymorphisms representing relevant gene pools. We present comprehensive genome resequencing data from a panel of 52 highly diverse natural and synthetic B. napus accessions, along with a stringently selected panel of 4.3 million high-confidence, genome-wide SNPs. The data is of great interest for genomics-assisted breeding and for evolutionary studies on the origins and consequences in allopolyploidisation in plants.
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Affiliation(s)
- Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Stadt Seeland 06466, Germany
| | - Birgit Samans
- Justus Liebig University, Department of Plant Breeding, Heinrich-Buff-Ring 26-32, Gießen 35392, Germany
| | | | - Chris Ulpinnis
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Stadt Seeland 06466, Germany
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Stadt Seeland 06466, Germany
| | - Doreen Stengel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Stadt Seeland 06466, Germany
| | - Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Stadt Seeland 06466, Germany
| | - Denis Lespinasse
- Syngenta France SAS, 12 chemin de l'Hobit, Saint-Sauveur 31790, France
| | - Zeljko Micic
- Deutsche Saatveredelung AG, Weissenburger Straße 5, Lippstadt 59557, Germany
| | - Stefan Abel
- Limagrain GmbH, Salder Str. 4, Peine 31226, Germany
| | - Peter Duchscherer
- Bayer Crop Science AG, Streichmühler Str. 8, Grundhof 24977, Germany
| | - Frank Breuer
- KWS Saat AG, Grimsehlstr. 31, Einbeck 37555, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth-Hof, Holtsee 24363, Germany
| | - Gunhild Leckband
- German Seed Alliance GmbH, Neue Schönholzer Str. 12, Berlin 13187, Germany
| | - Rod Snowdon
- Justus Liebig University, Department of Plant Breeding, Heinrich-Buff-Ring 26-32, Gießen 35392, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Stadt Seeland 06466, Germany
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11
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Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G, Sameri M, Azhaguvel P, Sakuma S, Dhanagond S, Sharma R, Mascher M, Himmelbach A, Gottwald S, Nair SK, Tagiri A, Yukuhiro F, Nagamura Y, Kanamori H, Matsumoto T, Willcox G, Middleton CP, Wicker T, Walther A, Waugh R, Fincher GB, Stein N, Kumlehn J, Sato K, Komatsuda T. Evolution of the Grain Dispersal System in Barley. Cell 2015; 162:527-39. [PMID: 26232223 DOI: 10.1016/j.cell.2015.07.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/13/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
About 12,000 years ago in the Near East, humans began the transition from hunter-gathering to agriculture-based societies. Barley was a founder crop in this process, and the most important steps in its domestication were mutations in two adjacent, dominant, and complementary genes, through which grains were retained on the inflorescence at maturity, enabling effective harvesting. Independent recessive mutations in each of these genes caused cell wall thickening in a highly specific grain "disarticulation zone," converting the brittle floral axis (the rachis) of the wild-type into a tough, non-brittle form that promoted grain retention. By tracing the evolutionary history of allelic variation in both genes, we conclude that spatially and temporally independent selections of germplasm with a non-brittle rachis were made during the domestication of barley by farmers in the southern and northern regions of the Levant, actions that made a major contribution to the emergence of early agrarian societies.
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Affiliation(s)
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Natesan Senthil
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Guoxiong Chen
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Mohammad Sameri
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Perumal Azhaguvel
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Shun Sakuma
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Sidram Dhanagond
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Rajiv Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Sven Gottwald
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Sudha K Nair
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Fumiko Yukuhiro
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Yoshiaki Nagamura
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan
| | - George Willcox
- Archéorient CNRS UMR 5133, Université de Lyon II, Jalés, Berrias 07460, France
| | | | - Thomas Wicker
- Institute of Plant Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Alexander Walther
- Department of Earth Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Robbie Waugh
- University of Dundee, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Geoffrey B Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Glen Osmond, SA 5066, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 710-0046 Kurashiki, Japan
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, 305-8602 Tsukuba, Japan.
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12
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Aliyeva-Schnorr L, Beier S, Karafiátová M, Schmutzer T, Scholz U, Doležel J, Stein N, Houben A. Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:385-394. [PMID: 26332657 DOI: 10.1111/tpj.13006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination-poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.
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Affiliation(s)
- Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Miroslava Karafiátová
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
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13
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Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides. Genetics 2015; 200:771-9. [PMID: 25971668 DOI: 10.1534/genetics.115.177642] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022] Open
Abstract
Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization (FISH). We developed three different probes with each containing 23,000-27,000 oligos. These probes spanned 8.3-17 Mb of DNA on targeted cucumber chromosomes and had the densities of 1.5-3.2 oligos per kilobases. These probes produced FISH signals on a single cucumber chromosome and were used to paint homeologous chromosomes in other Cucumis species diverged from cucumber for up to 12 million years. The bulked oligo probes allowed us to track a single chromosome in early stages during meiosis. We were able to precisely map the pairing between cucumber chromosome 7 and chromosome 1 of Cucumis hystrix in a F1 hybrid. These two homeologous chromosomes paired in 71% of prophase I cells but only 25% of metaphase I cells, which may provide an explanation of the higher recombination rates compared to the chiasma frequencies between homeologous chromosomes reported in plant hybrids.
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14
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Poursarebani N, Ma L, Schmutzer T, Houben A, Stein N. FISH Mapping for Physical Map Improvement in the Large Genome of Barley: A Case Study on Chromosome 2H. Cytogenet Genome Res 2014; 143:275-9. [DOI: 10.1159/000366028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 11/19/2022] Open
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15
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014; 15:R78. [PMID: 24917130 PMCID: PMC4073093 DOI: 10.1186/gb-2014-15-6-r78] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/10/2014] [Indexed: 01/02/2023] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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16
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014. [PMID: 24917130 DOI: 10.1186/gb‐2014‐15‐6‐r78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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17
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PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proc Natl Acad Sci U S A 2014; 111:2104-9. [PMID: 24481254 DOI: 10.1073/pnas.1320362111] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein disulfide isomerases (PDIs) catalyze the correct folding of proteins and prevent the aggregation of unfolded or partially folded precursors. Whereas suppression of members of the PDI gene family can delay replication of several human and animal viruses (e.g., HIV), their role in interactions with plant viruses is largely unknown. Here, using a positional cloning strategy we identified variants of PROTEIN DISULFIDE ISOMERASE LIKE 5-1 (HvPDIL5-1) as the cause of naturally occurring resistance to multiple strains of Bymoviruses. The role of wild-type HvPDIL5-1 in conferring susceptibility was confirmed by targeting induced local lesions in genomes for induced mutant alleles, transgene-induced complementation, and allelism tests using different natural resistance alleles. The geographical distribution of natural genetic variants of HvPDIL5-1 revealed the origin of resistance conferring alleles in domesticated barley in Eastern Asia. Higher sequence diversity was correlated with areas with increased pathogen diversity suggesting adaptive selection for bymovirus resistance. HvPDIL5-1 homologs are highly conserved across species of the plant and animal kingdoms implying that orthologs of HvPDIL5-1 or other closely related members of the PDI gene family may be potential susceptibility factors to viruses in other eukaryotic species.
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