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      Draft Genome Sequence of the Symbiotic Frankia sp. strain B2 isolated from root nodules of Casuarina cunninghamiana found in Algeria


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          Frankia sp. strain B2 was isolated from Casuarina cunninghamiana nodules . Here, we report the 5.3-Mbp draft genome sequence of Frankia sp. strain B2 with a G+C content of 70.1 % and 4,663 candidate protein-encoding genes. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.

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          Rapid isolation of high molecular weight plant DNA.

          A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.
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            antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

            Abstract Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
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              Solexa Ltd.

              Solexa Ltd is developing an integrated system, based on a breakthrough single molecule sequencing technology, to address a US$2 billion market that is expected to grow exponentially alongside and as a consequence of further technological enhancements. The system, software and consumables will initially be sold to research organizations, pharmaceutical companies and diagnostic companies that will sequence large regions of genomic DNA, including whole genomes, at costs several orders of magnitude below current levels. Solexa expects to launch its first product in 2006, and as it continues to make time and cost efficiencies, additional products will be launched into the expanding markets that will have broad applications in basic research through to healthcare management.

                Author and article information

                J Genomics
                J Genomics
                Journal of Genomics
                Ivyspring International Publisher (Sydney )
                19 January 2020
                : 8
                : 11-15
                [1 ]Laboratoire de Biologie du Sol, Faculté des Sciences Biologiques, Université des Sciences et de la Technologies Houari Boumediene (USTHB), BP32 El Alia - Bab Ezzouar Algiers, Algeria.
                [2 ]University of New Hampshire, 46 College Rd., Durham, New Hampshire, USA, 03824-2617
                [3 ]Laboratoire des Symbioses Tropicales et Méditerranéennes (IRD/INRA/CIRAD/Université de Montpellier/Supagro), 34398 Montpellier Cedex 5, France.
                [4 ]Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM) UMR 7245 CNRS-MNHN), Museum national d'Histoire naturelle, Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005 Paris, France
                Author notes
                ✉ Corresponding authors: Louis S. Tisa Mailing address: Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd., Durham, NH 03824-2617. Email: louis.tisa@ 123456unh.edu Telephone: 1-603-862-2442 Fax: 1-603-862-2621 and Hassen Gherbi Mailing address: LSTM-Laboratoire des Symbioses Tropicales & Méditerranéennes (IRD-CIRAD-INRA-UM-SupAgro), Campus International de Baillarguet, TA A-82/J. 34398 Montpellier Cedex 5 France. Email: hassen.gherbi@ 123456ird.fr . Telephone: +33 (0)4 67 59 37 45. Fax: +33 (0)4 67 59 38 02

                Competing Interests: The authors have declared that no competing interest exists.

                © The author(s)

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions.

                : 16 July 2019
                : 22 November 2019
                Research Paper

                actinorhizal symbiosis,host-microbe interactions,nitrogen fixation,casuarinaceae, frankia,land reclamation,genomes


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