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      The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

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          Abstract

          Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx. This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed.

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          Most cited references 45

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          Toward almost closed genomes with GapFiller

          De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
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            The Universal Protein Resource (UniProt)

            The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The UniProt Consortium is a collaboration between the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Knowledgebase, the UniProt Reference Clusters, the UniProt Archive and the UniProt Metagenomic and Environmental Sequences database. UniProt is updated and distributed every three weeks, and can be accessed online for searches or download at http://www.uniprot.org.
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              A beginner's guide to eukaryotic genome annotation.

              The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. Although annotating a eukaryotic genome assembly is now within the reach of non-experts, it remains a challenging task. Here we provide an overview of the genome annotation process and the available tools and describe some best-practice approaches.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                02 March 2020
                May 2020
                : 10
                : 5
                : 1457-1467
                Affiliations
                [* ]Ecology, Evolution, and Organismal Biology Dept., Iowa State University, Ames, IA, 50010
                []State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center, Nanjing Agricultural University, Nanjing, 210095, China
                []College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
                [§ ]Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University
                [** ]Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63110
                [†† ]Department of Soil and Crop Sciences, Texas A&M University, College Station, 77843
                [‡‡ ]USDA/Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX 77845
                [§§ ]Department of Genetics, University of Georgia, Athens, GA 30602
                Author notes
                [1 ]Corresponding author: Crop Germplasm Research Unit, USDA-ARS, 2881 F&B Road, College Station, TX 77845. E-mail: Joshua.Udall@ 123456usda.gov
                Article
                GGG_401050
                10.1534/g3.120.401050
                7202014
                32122962
                Copyright © 2020 Grover et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 3, Tables: 5, Equations: 0, References: 91, Pages: 11
                Product
                Categories
                Genome Report

                Genetics

                gossypium longicalyx, nematode resistance, cotton fiber, genome sequence, pacbio

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