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      The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

      research-article
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      Nature Genetics
      Nature Publishing Group US
      Genomics, DNA sequencing

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          Abstract

          High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement.

          Abstract

          High-quality genome sequence of cultivated peanut comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut.

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          Most cited references50

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          The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

          The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
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            Profile hidden Markov models.

            S. Eddy (1998)
            The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.
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              QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations.

              The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps. © 2013 The Authors The Plant Journal © 2013 Blackwell Publishing Ltd.
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                Author and article information

                Contributors
                weijianz@fafu.edu.cn
                wangxiyin@vip.sina.com
                rayming@illinois.edu
                r.k.varshney@cgiar.org
                Journal
                Nat Genet
                Nat. Genet
                Nature Genetics
                Nature Publishing Group US (New York )
                1061-4036
                1546-1718
                1 May 2019
                1 May 2019
                2019
                : 51
                : 5
                : 865-876
                Affiliations
                [1 ]ISNI 0000 0004 1760 2876, GRID grid.256111.0, Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Oil Crops Research Institute, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, , Fujian Agriculture and Forestry University, ; Fuzhou, China
                [2 ]GRID grid.459813.2, Nextomics Biosciences Institute, ; Wuhan, China
                [3 ]ISNI 0000 0004 1760 2876, GRID grid.256111.0, Haixia Institute of Science and Technology, , Fujian Agriculture and Forestry University, ; Fuzhou, China
                [4 ]ISNI 0000 0004 1936 8091, GRID grid.15276.37, Agronomy Department, , University of Florida, ; Gainesville, FL USA
                [5 ]ISNI 0000 0000 9323 1772, GRID grid.419337.b, Center of Excellence in Genomics & Systems Biology, , International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), ; Hyderabad, India
                [6 ]ISNI 0000 0004 0532 3255, GRID grid.64523.36, College of Biosciences and Biotechnology, , National Cheng Kung University, ; Tainan, Taiwan
                [7 ]ISNI 0000 0001 2287 1366, GRID grid.28665.3f, Graduate Program in Translational Agricultural Sciences, , National Cheng Kung University and Academia Sinica, ; Taipei, Taiwan
                [8 ]ISNI 0000 0004 0415 7259, GRID grid.452720.6, Guangxi Academy of Agricultural Sciences, ; Nanning, China
                [9 ]ISNI 0000 0004 0644 6150, GRID grid.452757.6, Biotechnology Research Center, , Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, ; Shandong, China
                [10 ]ISNI 0000 0001 0707 0296, GRID grid.440734.0, North China University of Science and Technology, ; Tangshan, China
                [11 ]ISNI 0000 0004 1936 7910, GRID grid.1012.2, The University of Western Australia, ; Perth, Western Australia Australia
                [12 ]ISNI 0000 0004 0404 0958, GRID grid.463419.d, USDA-ARS, Crop Protection and Management Research Unit, ; Tifton, GA USA
                [13 ]ISNI 0000 0001 0627 4537, GRID grid.495707.8, Henan Academy of Agricultural Sciences, ; Zhengzhou, China
                [14 ]ISNI 0000 0004 1757 9469, GRID grid.464406.4, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, ; Wuhan, China
                [15 ]GRID grid.449900.0, Zhongkai University of Agriculture and Engineering, ; Guangzhou, China
                [16 ]ISNI 0000 0004 1760 2876, GRID grid.256111.0, College of Crop Sciences, , Fujian Agriculture and Forestry University, ; Fuzhou, China
                [17 ]ISNI 0000 0001 0662 3178, GRID grid.12527.33, School of Life Science, , TsingHua University, ; Beijing, China
                [18 ]ISNI 0000 0001 0472 9649, GRID grid.263488.3, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, , Shenzhen University, ; Shenzhen, China
                [19 ]ISNI 0000 0001 0707 9354, GRID grid.265253.5, Tuskegee University, ; Tuskegee, AL USA
                [20 ]ISNI 0000 0001 1456 3750, GRID grid.412419.b, Osmania University, ; Hyderabad, India
                [21 ]ISNI 0000 0004 0532 0580, GRID grid.38348.34, College of Life Science, , National Tsing Hua University, ; Hsin Chu, Taiwan
                [22 ]ISNI 0000 0004 1936 738X, GRID grid.213876.9, Plant Genome Mapping Laboratory, , University of Georgia, ; Athens, GA USA
                [23 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, Department of Plant Biology, , University of Illinois of Urbana-Champaign, ; Urbana, IL USA
                Author information
                http://orcid.org/0000-0002-1340-5723
                http://orcid.org/0000-0002-2672-3069
                http://orcid.org/0000-0002-0259-1508
                http://orcid.org/0000-0002-4101-6530
                http://orcid.org/0000-0002-0236-9624
                http://orcid.org/0000-0002-0347-1516
                http://orcid.org/0000-0001-5531-7273
                http://orcid.org/0000-0002-3460-8570
                http://orcid.org/0000-0001-9734-8123
                http://orcid.org/0000-0002-3282-9441
                http://orcid.org/0000-0002-0142-5495
                http://orcid.org/0000-0003-1556-1436
                http://orcid.org/0000-0002-4955-4763
                http://orcid.org/0000-0002-5564-3041
                http://orcid.org/0000-0001-7465-7425
                http://orcid.org/0000-0003-3277-9808
                http://orcid.org/0000-0001-8720-0133
                http://orcid.org/0000-0003-1665-3519
                http://orcid.org/0000-0001-5066-6052
                http://orcid.org/0000-0002-5576-4978
                http://orcid.org/0000-0002-9413-408X
                http://orcid.org/0000-0002-8999-4894
                http://orcid.org/0000-0003-2159-0487
                http://orcid.org/0000-0003-3454-0374
                http://orcid.org/0000-0002-9417-5789
                http://orcid.org/0000-0002-4562-9131
                Article
                402
                10.1038/s41588-019-0402-2
                7188672
                31043757
                f0ab6bc9-8ad1-40a8-a6c3-23020719009f
                © The Author(s), under exclusive licence to Springer Nature America, Inc. 2019

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 9 September 2018
                : 22 March 2019
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                © The Author(s), under exclusive licence to Springer Nature Limited 2019

                Genetics
                genomics,dna sequencing
                Genetics
                genomics, dna sequencing

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