Abstract
We report the 9.0-Mb draft genome of Amycolatopsis vancoresmycina strain DSM 44592T, isolated from Indian soil sample; produces antibiotic vancoresmycin. Draft genome of strain DSM44592T consists of 9,037,069 bp with a G+C content of 71.79% and 8340 predicted protein coding genes and 57 RNAs. RAST annotation indicates that strains Streptomyces sp. AA4 (score 521), Saccharomonospora viridis DSM 43017 (score 400) and Actinosynnema mirum DSM 43827 (score 372) are the closest neighbors of the strain DSM 44592T.
Keywords: Amycolatopsis vancoresmycina strain DSM 44592T, Illumina-HiSeq, NGS QC toolkit, Rapid annotations using subsystems technology (RAST)
| Specifications | |
|---|---|
| Organism/cell line/tissue | Amycolatopsis vancoresmycina |
| Strain(s) | DSM 44592T |
| Sequencer or array type | Sequencer; the Illumina-HiSeq 1000 |
| Data format | Processed |
| Experimental factors | Microbial strain |
| Experimental features | Draft genome sequence of A. vancoresmycina strain DSM 44592T, assembly and annotation |
| Consent | n/a |
Direct link to the data
Direct link: http://www.ncbi.nlm.nih.gov/nuccore/AOUO00000000.
The genus Amycolatopsis was proposed by Lechevalier et al. [1]. Amycolatopsis vancoresmycina was proposed by Wink et al. [2]. A. vancoresmycina was isolated from Indian soil that produces novel glycopeptide antibiotics and a polyenic compound. A. vancoresmycina strain DSM 44592T which was isolated from soil [2], was obtained from an open collection of the German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig, Germany, deposited by Prof. Joachim M. Wink. Strain A. vancoresmycina DSM 44592T is Gram-positive bacteria, aerial mycelium with color ranged from brown beige to saffron yellow. Its peptidoglycan contains meso-diaminopimelic acid; diagnostic sugars are arabinose and galactose, mycolic acids are absent; MK-9 (H4) is the principal menaquinone; phospholipids are phosphatidylethanolamine, hydroxyl phosphatidylethanolamine, diphospha-tidylglycerol and phosphatidylinositol. Genomic DNA was extracted from a 48 hour old culture using ZR Fungal/Bacterial DNA MiniPrep™ as per manufacturer's instructions. The genome of A. vancoresmycina strain DSM 44592T was sequenced using the Illumina-HiSeq 1000 paired-end technology produced a total of 62,283,914 paired-end reads (insert size of 350 bp) of 101 bp. We have used NGS QC toolkit v2.3 [3] to filter the data for high quality (cut off read length for HQ = 70%, cut off quality score = 20), vector/adaptor free reads for genome assembly. A total of 57,704,188 high quality, vector filtered reads (~ 647.6 times coverage) were used for assembly with SOAPdenovo v1.05 (at hash length of 69) followed by GapCloser (at hash length 15) software [4]. The final assembly contains 786 contigs of total size 9,037,069 bp, with N50 contig length of 18.4 kb; the largest contigs assembled measures 87.7 kb. This draft genome comprising 9,037,069 nt was annotated with the help of RAST (Rapid Annotation using Subsystem Technology) system [5] server. A total of 8340 predicted coding regions (CDSs), 3 rRNAs and 54 tRNAs were predicted.
RAST annotation indicates that strain Streptomyces sp. AA4 (score 521), Saccharomonospora viridis DSM 43017 (score 400) and Actinosynnema mirum DSM 43827 (score 372) are the closest neighbors of the strain DSM 44592T. Genome annotation available at RAST indicates that the strain DSM 44592T contains the genes for glycolysis and gluconeogenesis, TCA cycle and pentose phosphate pathway. Genes of alkaline phosphatase, galactosidase (alpha and beta subunit), mannosidase (alpha and beta subunits), catalase (EC 1.11.1.6) and ferroxidase (EC 1.16.3.1) are also present in the genome annotation of strain 44592T. We have mapped all predicted 8340 CDSs to KEGG pathways [6] with the help of KASS server [7] and found that genes of rifA, rifB, rifC, rifD, rifJ, rifK, rifL, rifM and rifN are present in the genome, mapped on the ansamycins biosynthesis pathway. Genes of glucose-1-phosphate thymidylyltransferase [EC:2.7.7.24], dTDP-glucose 4,6-dehydratase [EC:4.2.1.46], dTDP-4-dehydrorhamnose reductase [EC:1.1.1.133] and dTDP-4-dehydrorhamnose 3,5-epimerase [EC:5.1.3.13] are present and mapped at the pathway of polyketide sugar unit biosynthesis (Fig. 1).
Fig. 1.
Sub-system distribution of strain Amycolatopsis vancoresmycina strain DSM 44592T (based on RAST annotation server).
Nucleotide sequence accession number
The A. vancoresmycina DSM 44592T whole genome shot gun (WGS) project has been deposited at DDBJ/EMBL/GenBank under the project accession AOUO00000000 of the project (01) has the accession numbers AOUO01000000 and consists of sequences AOUO01000001 AOUO01000784.
Conflict of interest
The authors declare that there is no conflict of interest on any work published in this paper.
Acknowledgments
This work was funded by IMTECH-CSIR. NK is supported by a research fellowship from the University Grant Commission (UGC) Govt. of India. SK is supported by a research fellowship from the Council of Scientific and Industrial Research. This is IMTECH communication number 108/2013.
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