Permanent Draft Genome sequence for Frankia sp. strain CcI49, a Nitrogen-Fixing Bacterium Isolated from Casuarina cunninghamiana that Infects Elaeagnaceae

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Abstract

Frankia sp. strain CcI49 was isolated from Casuarina cunninghamiana nodules . However the strain was unable to re-infect Casuarina, but was able to infect other actinorhizal plants including Elaeagnaceae. Here, we report the 9.8-Mbp draft genome sequence of Frankia sp. strain CcI49 with a G+C content of 70.5 % and 7,441 candidate protein-encoding genes. Analysis of the genome revealed the presence of a bph operon involved in the degradation of biphenyls and polychlorinated biphenyls.

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antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

Kai Blin, Thomas Wolf, Marc Chevrette … (2017)

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.

Simon Bennett (2004)

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.

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Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

Philippe Normand, Pascal Lapierre, Louis Tisa … (2007)

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%-98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.

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Author and article information

Journal

Journal ID (nlm-ta): J Genomics

Journal ID (iso-abbrev): J Genomics

Journal ID (publisher-id): jgen

Title: Journal of Genomics

Publisher: Ivyspring International Publisher (Sydney )

ISSN (Electronic): 1839-9940

Publication date Collection: 2017

Publication date (Electronic): 12 September 2017

Volume: 5

Pages: 119-123

Affiliations

[1 ]Suez Canal University, Ismailia, Egypt,

[2 ]University of New Hampshire, Durham, New Hampshire, USA.

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. Samira Mansour, Mailing address: Botany department, Faculty of Science, Suez Canal University, Ismailia, Egypt. Email: samirarmansour@ 123456hotmail.com

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

Article

Publisher ID: jgenv05p0119

DOI: 10.7150/jgen.22138

PMC ID: 5607709

SO-VID: f9562164-8430-4072-927e-39289debd09f

License:

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

History

Date received : 28 July 2017

Date accepted : 31 August 2017

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A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world
Authors: Fede Berckx, Thanh Nguyen, Cyndi Mae Bandong …

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Permanent Draft Genome sequence for Frankia sp . strain CcI49, a Nitrogen-Fixing Bacterium Isolated from Casuarina cunninghamiana that Infects Elaeagnaceae

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Most cited references 27

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

Solexa Ltd.

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

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