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      The giant diploid faba genome unlocks variation in a global protein crop

      research-article
      1 , 2 , 3 , 4 , 5 , 6 , 7 , 1 , 3 , 8 , 5 , 9 , 10 , 11 , 12 , 3 , 8 , 13 , 14 , 6 , 4 , 13 , 4 , 15 , 13 , 16 , 1 , 5 , 13 , 16 , 17 , 18 , 5 , 19 , 1 , 3 , 3 , 9 , 18 , 7 , 17 , 13 , 1 , 20 , 14 , 2 , 1 , 21 , 22 , 23 , 4 , 3 , 24 , 11 , 25 , 1 , 5 , , 17 , 18 , 23 , , 4 ,
      Nature
      Nature Publishing Group UK
      Plant genetics, Natural variation in plants, Plant breeding, Plant evolution, Genome evolution

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity 1 . However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value 2 . Faba bean ( Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.

          Abstract

          Using a high-quality chromosome-scale assembly of the faba bean genome, the genetic basis of seed size and hilum colour is explored.

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          Most cited references113

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              STAR: ultrafast universal RNA-seq aligner.

              Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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                Author and article information

                Contributors
                d.m.osullivan@reading.ac.uk
                alan.schulman@helsinki.fi
                sua@mbg.au.dk
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                8 March 2023
                8 March 2023
                2023
                : 615
                : 7953
                : 652-659
                Affiliations
                [1 ]GRID grid.418934.3, ISNI 0000 0001 0943 9907, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, ; Seeland, Germany
                [2 ]GRID grid.8664.c, ISNI 0000 0001 2165 8627, Department of Plant Breeding, , Justus Liebig University Giessen, ; Giessen, Germany
                [3 ]GRID grid.5613.1, ISNI 0000 0001 2298 9313, Agroécologie, INRAE, Institut Agro, , University Bourgogne, University Bourgogne Franche-Comté, ; Dijon, France
                [4 ]GRID grid.7048.b, ISNI 0000 0001 1956 2722, Department of Molecular Biology and Genetics, , Aarhus University, ; Aarhus C, Denmark
                [5 ]GRID grid.9435.b, ISNI 0000 0004 0457 9566, School of Agriculture, Policy and Development, University of Reading, ; Reading, UK
                [6 ]GRID grid.10979.36, ISNI 0000 0001 1245 3953, Department of Analytical Chemistry, Faculty of Science, , Palacky University, ; Olomouc, Czech Republic
                [7 ]GRID grid.7048.b, ISNI 0000 0001 1956 2722, Center for Quantitative Genetics and Genomics, , Aarhus University, ; Aarhus C, Denmark
                [8 ]Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria Australia
                [9 ]GRID grid.454748.e, Institute of Experimental Botany of the Czech Academy of Sciences, , Centre of the Region Haná for Biotechnological and Agricultural Research, ; Olomouc, Czech Republic
                [10 ]GRID grid.4567.0, ISNI 0000 0004 0483 2525, Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, , German Research Center for Environmental Health, ; Neuherberg, Germany
                [11 ]GRID grid.8385.6, ISNI 0000 0001 2297 375X, IBG-4 Bioinformatics Forschungszentrum Jülich, ; Jülich, Germany
                [12 ]GRID grid.440950.c, ISNI 0000 0001 2034 0967, Bingen Technical University of Applied Sciences, ; Bingen, Germany
                [13 ]GRID grid.448362.f, ISNI 0000 0001 0135 7552, Biology Centre, Czech Academy of Sciences, , Institute of Plant Molecular Biology, ; České Budějovice, Czech Republic
                [14 ]GRID grid.10979.36, ISNI 0000 0001 1245 3953, Department of Botany, Faculty of Science, , Palacky University, ; Olomouc, Czech Republic
                [15 ]Sejet Planteforædling, Horsens, Denmark
                [16 ]Nordic Seed, Odder, Denmark
                [17 ]GRID grid.22642.30, ISNI 0000 0004 4668 6757, Natural Resources Institute Finland (Luke), ; Helsinki, Finland
                [18 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Institute of Biotechnology, , University of Helsinki, ; Helsinki, Finland
                [19 ]GRID grid.425600.5, ISNI 0000 0004 0501 5041, KeyGene, ; Wageningen, The Netherlands
                [20 ]GRID grid.421064.5, ISNI 0000 0004 7470 3956, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, ; Leipzig, Germany
                [21 ]GRID grid.7450.6, ISNI 0000 0001 2364 4210, Center of Integrated Breeding Research (CiBreed), , Georg-August-University, ; Göttingen, Germany
                [22 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Department of Agricultural Sciences, , University of Helsinki, ; Helsinki, Finland
                [23 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Viikki Plant Science Centre, , University of Helsinki, Helsinki, Finland, ; Córdoba, Spain
                [24 ]GRID grid.425162.6, ISNI 0000 0001 2195 4653, Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Área de Mejora y Biotecnología, Centro Alameda del Obispo, ; Córdoba, Spain
                [25 ]GRID grid.411327.2, ISNI 0000 0001 2176 9917, Institute for Biological Data Science, CEPLAS, , Heinrich Heine University Düsseldorf, ; Düsseldorf, Germany
                Author information
                http://orcid.org/0000-0003-2951-0541
                http://orcid.org/0000-0002-9711-4826
                http://orcid.org/0000-0002-8502-9210
                http://orcid.org/0000-0001-7070-6015
                http://orcid.org/0000-0002-7447-6226
                http://orcid.org/0000-0001-8757-9905
                http://orcid.org/0000-0002-5858-8105
                http://orcid.org/0000-0003-3972-7058
                http://orcid.org/0000-0002-3418-3840
                http://orcid.org/0000-0001-7787-1849
                http://orcid.org/0000-0002-6757-0943
                http://orcid.org/0000-0002-8229-8693
                http://orcid.org/0000-0001-9024-7717
                http://orcid.org/0000-0002-4653-1195
                http://orcid.org/0000-0003-0558-1425
                http://orcid.org/0000-0001-6711-6639
                http://orcid.org/0000-0002-6643-8019
                http://orcid.org/0000-0003-3215-9481
                http://orcid.org/0000-0002-5068-9681
                http://orcid.org/0000-0003-3125-3695
                http://orcid.org/0000-0002-9281-0443
                http://orcid.org/0000-0002-0482-2592
                http://orcid.org/0000-0002-1867-5730
                http://orcid.org/0000-0002-6263-0492
                http://orcid.org/0000-0002-7807-2966
                http://orcid.org/0000-0001-9804-1529
                http://orcid.org/0000-0002-5202-8764
                http://orcid.org/0000-0003-0829-1570
                http://orcid.org/0000-0001-6373-6013
                http://orcid.org/0000-0002-6117-8510
                http://orcid.org/0000-0001-5577-7616
                http://orcid.org/0000-0003-3011-8731
                http://orcid.org/0000-0002-8097-5750
                http://orcid.org/0000-0002-2907-4287
                http://orcid.org/0000-0003-0921-8041
                http://orcid.org/0000-0003-4889-056X
                http://orcid.org/0000-0002-4126-6177
                http://orcid.org/0000-0002-1096-1468
                Article
                5791
                10.1038/s41586-023-05791-5
                10033403
                36890232
                d6c23929-80ec-4aec-9563-11054d7bc09b
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 23 September 2022
                : 3 February 2023
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                © The Author(s), under exclusive licence to Springer Nature Limited 2023

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                plant genetics,natural variation in plants,plant breeding,plant evolution,genome evolution

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