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Draft Genome Sequence of an Extensively Drug-Resistant
Mycobacterium tuberculosis Clinical Isolate of the Ural Strain
OSDD493
Shamsudheen Karuthedath Vellarikkal,a Ajay Vir Singh,c Pravin Kumar Singh,c Parul Garg,c Viswa Mohan Katoch,c Kiran Katoch,c
Open Source Drug Discovery Consortium,d D. S. Chauhan,c Vinod Scaria,b Sridhar Sivasubbua
Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, Indiaa; GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, Indiab; National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, Indiac; CSIR Open Source Drug Discovery Unit, Anusandhan Bhavan, New Delhi, Indiad We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium tuberculosis belonging to the Ural strain
OSDD493 from India.
Received 2 October 2013 Accepted 4 October 2013 Published 7 November 2013
Citation Karuthedath Vellarikkal S, Vir Singh A, Kumar Singh P, Garg P, Mohan Katoch V, Katoch K, Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S.
2013. Draft genome sequence of an extensively drug-resistant Mycobacterium tuberculosis clinical isolate of the Ural strain OSDD493. Genome Announc. 1(6):e00928-13. doi:
10.1128/genomeA.00928-13.
Copyright 2013 Karuthedath Vellarikkal et al. This is an open-access article distributed under the terms of
Address correspondence to Sridhar Sivasubbu, s.sivasubbu@igib.res.in, or Vinod Scaria, vinods@igib.res.in.
Tuberculosis is caused by a closely related group of pathogenic CLCGenomicsWorkbench6.Theassemblyresultedin193contigsat
organisms known as the Mycobacterium tuberculosis complex.
N50 values of 42,650 bp and a total assembly of 4,227,747 bp. Further, Distinct lineages of Mycobacterium tuberculosis have been reported automated gene prediction on the draft genomes was performed us- and have been characterized and classified based on spoligotype pat- ing the RAST server Analysis revealed 4,223 genes, including 42 terns. The six major distinct lineages are the Indo-Oceanic (EAI), East Asian (Beijing), East African-Indian (CAS), Euro-American (Haar- Nucleotide sequence accession numbers. This whole-genome
lem, LAM, T, X), West African I (AFRI1), and West African lineage II shotgun project has been deposited at DDBJ/EMBL/GenBank un- (AFRI2) lineages The Ural spoligotype was initially identified der the accession number The version described from the Ural region in Russia, which has one of the highest inci- in this paper is version AVQJ01000000.
dences of tuberculosis in the country. Nevertheless, the Ural spoligo-type forms a minority of genotypes of M. tuberculosis strains isolated ACKNOWLEDGMENTS
from this region The genotype has also been reported from across We thank Swati Subodh (TCGA) and Nupur Mehrotra (Premas Biotech) Eurasia and Central Asia and forms a significant proportion of geno- for scientific discussions and help in maintaining the strains. We also types observed in some of these regions. The Ural genotype is thought acknowledge S. Ramachandran for valuable input.
to be associated with significantly low transmissibility, pathogenicity, The project was funded by CSIR India through the Open Source Drug Discovery Programme (HCP001). The sequencing facility is supported Understanding the genome sequence of the Ural strain of Myco- through grants SIP006 and FAC002 from CSIR, India, and the computa- bacterium tuberculosis would provide immense insights into the tional analysis was performed at the CSIR Center for In Silico Biology at genomic architecture associated with low pathogenicity. In this pa- per, we describe the draft genome sequence of an extensively drug-resistant clinical isolate of Mycobacterium tuberculosis conforming to REFERENCES
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