Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria
© The Author(s). 2016
Received: 10 May 2016
Accepted: 27 August 2016
Published: 9 September 2016
The members of the genus Thermoactinomyces are known for their protein degradative capacities. Thermoactinomyces sp. strain AS95 is a Gram-positive filamentous bacterium, isolated from moderately saline water in the Thamelaht region of Algeria. This isolate is a thermophilic aerobic bacterium with the capacity to produce extracellular proteolytic enzymes. This strain exhibits up to 99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA gene sequence similarity. Here we report on the phenotypic features of Thermoactinomyces sp. strain AS95 together with the draft genome sequence and its annotation. The genome of this strain is 2,558,690 bp in length (one chromosome, but no plasmid) with an average G + C content of 47.95 %, and contains 2550 protein-coding and 60 RNA genes together with 64 ORFs annotated as proteases.
Modern metagenomic approaches have provided insights on the evolution and functional capacity of microbial communities resistant to classical culture-based methods . However, these classical techniques remain crucial for understanding the molecular adaptations of microbial guilds, especially those with potential biotechnological applications [2, 3]. Consequently, efforts to isolate novel taxa, particularly from environmentally extreme habitats remain widespread [4, 5].
The genus Thermoactinomyces is a member of the family Thermoactinomycetaceae . The first known representative from this genus ( Thermoactinomyces vulgaris ) was isolated from decaying straw and manure . Since then, a number of isolates, from a wide array of extreme habitats [7–10] have been validly described. Currently, this genus comprises ten validly published species, and a few of these are; Thermoactinomyces vulgaris , Thermoactinomyces intermedius , Thermoactinomyces daqus  and Thermoactinomyces guangxiensis . These species are all Gram-positive, aerobic, non-acid-fast, chemoorganotrophic, filamentous and thermophilic bacteria.
Here, we report the draft genome sequence of Thermoactinomyces sp. strain AS95, which was isolated from a sebkha (endorheic salt pan) in the Thamelaht region of Algeria. We present a summary of the classification and set of phenotypic features for Thermoactinomyces sp. strain AS95 together with the description of the non-contiguous genome sequence and its annotation with particular reference to ORFs encoding proteolytic enzymes.
Classification and features
Classification and general features of Thermoactinomyces sp. strain AS95
Species: Thermoactinomyces sp.
Endospores on unbranched sporophores
40–65 °C (Thermophilic)
pH range; Optimum
5.0 % total salt (w/v)
Sample collection time
20 June 2013
890 m above sea level
The strain was cultivated on Thermus medium agar containing 2.0 g NaCl, 4.0 g yeast extract, 8.0 g peptone and 30.0 g agar per liter of distilled water. The bacterium grew optimally at 55 °C, with a broad temperature growth range of between 40 and 65 °C (Table 1). The strain grew in liquid media at pH values from 5.6 to 8.6, but optimal growth occurred at a pH of 7.2. Morphologically, the isolate forms white colonies and abundant aerial mycelia with the appearance of well-developed, branched and septate substrate mycelia. The micromorphology of the cells was examined using scanning electron microscopy (Fig. 1). The predominant menaquinone was MK-7. Major fatty acids included iso-C15:0, and significant amounts of iso-C17:0 were also present.
Genome sequencing information
Genome project history
One paired-end 300 bp library
Gene calling method
NCBI Prokaryotic Genome, Annotation Pipeline
Genbank Date of Release
April 04, 2016
Growth conditions and genomic DNA preparation
Thermoactinomyces sp. strain AS95 was grown aerobically on Thermus medium agar (pH 7.2) at 55 °C for 24 h. Genomic DNA was extracted using a modification of a previously described protocol . The quantity and quality of the genomic DNA was measured using a NanoDrop Spectrophotometer and a Qubit™ Fluorometer (Thermo Fisher Scientific Inc.).
Genome sequencing and assembly
Genomic DNA samples of Thermoactinomyces sp. strain AS95 were sequenced at MR DNA (Shallowater, TX, USA). Genome sequencing was performed on a MiSeq (Illumina, Inc.) generating 2 x 300 bp paired-end libraries. The sequencing run produced a total of 5,085,250 reads, with a mean length of 265.58 bp. The raw paired-end sequences were subjected to the fastxtools software  for quality trimming using a phred quality score ≥ 20. After trimming, a total of 3,013,639 reads with a mean length of 171.11 bp were assembled using SPAdes, version 3.5.0 . The final assembly resulted in a total of 11 scaffolds, which generated a genome size of 2.56 Mb.
Genome annotation was carried out on the RAST server  and using the NCBI Prokaryotic Genome Annotation Pipeline tools . This Whole Genome Shotgun sequence project has been deposited at DDBJ/EMBL/GenBank under accession LSVF00000000. The version described in this paper is version LSVF00000000.
Genome statistics of the Thermoactinomyces sp. strain AS95
% of totala
Genome size (bp)
DNA coding region (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes with Pfam domains
Genes assigned to COGs
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
% of totala
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
The four major types of proteases predicted in Thermoactinomyces sp. strain AS95
This study describes the draft genome sequence of Thermoactinomyces sp. strain AS95, which is associated with a high level of extracellular proteolytic activities. To date, only a few metabolic pathways involved in protein degradation have been characterized for the genus Thermoactinomyces . The genome sequence and characteristics of strain AS95 will provide new insights into the mechanisms of protein degradation in the genus Thermoactinomycetes, and towards establishing a comprehensive genomic catalog of the metabolic diversity of the genus Thermoactinomyces .
We wish to acknowledge the following organizations for providing financial support for this project: The Genomics Research Institute and the University of Pretoria (OKIB, DAC, TPM), the National Research Foundation (MWVG, DAC, TPM). The Algerian Ministry of Higher Education and Scientific Research is also acknowledged for funding (MAG and KK).
OKIB performed the analysis, and led the drafting of the manuscript. MAG isolated the strain and conducted confirmatory analysis using 16S rRNA gene sequencing. RP performed the assembly and annotation. MWVG performed the SEM and helped draft the manuscript. KK supervised the isolation of the strain. DAC provided support in drafting the manuscript. TPM conceived the study and provided support in drafting the manuscript. All authors read and approved the final version of the manuscript.
The authors declare that they have no competing interests.
Open AccessThis article is 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 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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