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      Genome Sequence of Aspergillus aculeatinus IC_8, Isolated from an Indoor Air Sample of an Urban Housing Complex in Abidjan, Ivory Coast

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          Abstract

          Aspergillus aculeatinus is an industrially important species of Aspergillus section Nigri capable of producing bioactive, antibiotic, and antitumor compounds. We sequenced the genome of a strain of A. aculeatinus that was isolated from the interior of a housing complex in Abidjan, Ivory Coast.

          ABSTRACT

          Aspergillus aculeatinus is an industrially important species of Aspergillus section Nigri capable of producing bioactive, antibiotic, and antitumor compounds. We sequenced the genome of a strain of A. aculeatinus that was isolated from the interior of a housing complex in Abidjan, Ivory Coast.

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          Most cited references 13

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          SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

          The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

             Marcel Martin (2011)
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              FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

              Background We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. Methodology/Principal Findings Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the “CAT” approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100–1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. Conclusions/Significance FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                Microbiol Resour Announc
                Microbiol Resour Announc
                ga
                mra
                MRA
                Microbiology Resource Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2576-098X
                11 March 2021
                March 2021
                : 10
                : 10
                Affiliations
                [a ]Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
                [b ]Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
                [c ]Parasitology and Mycology Department, Institut Pasteur de Côte d’Ivoire, Abidjan, Ivory Coast
                [d ]Aspergillus Unit, Institut Pasteur, Paris, France
                [e ]Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
                Vanderbilt University
                Author notes
                Address correspondence to John G. Gibbons, jggibbons@ 123456umass.edu .

                Citation Zhao S, Koffi D, Latge J-P, Sylla K, Gibbons JG. 2021. Genome sequence of Aspergillus aculeatinus IC_8, isolated from an indoor air sample of an urban housing complex in Abidjan, Ivory Coast. Microbiol Resour Announc 10:e00096-21. https://doi.org/10.1128/MRA.00096-21.

                Article
                MRA00096-21
                10.1128/MRA.00096-21
                7953289
                33707326
                Copyright © 2021 Zhao et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                Page count
                Figures: 1, Tables: 0, Equations: 0, References: 13, Pages: 3, Words: 1387
                Product
                Funding
                Funded by: HHS | National Institutes of Health (NIH), https://doi.org/10.13039/100000002;
                Award ID: R21AI137485
                Award Recipient :
                Categories
                Genome Sequences
                Custom metadata
                March 2021

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