Draft Genome of Mycobacterium Leprae Strain 7935681
<p>We report the assembled draft genome of Mycobacterium leprae strain 7935681 using HiSeq 2000. The genome size obtained was 3.27 Mb. Based on the gene prediction, total genes identified were 5,128, which includes CDS, tRNA and rRNA.</p>
Opinion
Mycobacterium leprae infection causes human leprosy. Leprosy is a chronic disease caused by a slow multiplying bacillus, Mycobacterium leprae. This mainly affects skin, damages nerve respiratory tract, eyes and eventually permanent disability [1]. Leprosy is known to occur at all ages ranging from early infancy to very old age. M. leprae, has a unique host cell tropism which infects and grows with in Schwann cells surrounding the axons of nerve cells. This tropism is considered to contribute to the pathology of leprosy. The biggest challenge is the fact that M. leprae cannot be cultured by normal methods. On a more positive note, the genome of M. leprae has been sequenced [2].
Assembly statistics Genome assembly size (Mbp) 3.27 Sequencing read coverage depth (fold) 200X Number of scaffolds 112 avg scaffold 29266 Scaffold N50 (bp) 46192 Max scaffold size (bp) 257291 Min scaffold size (bp) 1508 Annotation statistics Opinion Whole genome sequencing of M.leprae strain 7935681 was carried out using HiSeq 2000 with 2x100 bp chemistry. The raw data generated was quality filtered using Trimmomatic v 0.35 [3]. High quality reads were assembled using AbySS (Version: 1.5.2) [4] and SSPACE (Version: 3.0) [5] generating 112 scaffolds with an assembly size of 3.27 MB and N50 of 46,192 bp as shown in Table 1. This assembly was found to be the first assembly submitted in NCBI for the strains of M.leprae strain 7935681. The genome showed 57.7 % of G+C. The annotation was carried out using RAST server [6]. Total of 5,080 coding genes were predicted with 48 RNA genes which includes, 3 rRNA and 45 tRNA.
- Number of genes
- 5128
- Average gene length (bp)
- 434.8
- CDS
- 5046 rRNA
- 3 tRNA
- 45
Table 1: M.leprae strain 7935681 genome features
Bioinformatics & Proteomics Open Access Journal
Genomics has provided insights into the genes, pseudogenes and genetics of M. leprae, and its human host. Our future work is to find the phylogenic placement of this strain. In order to challenge the phylogenetic model it’s important to sequence more M. leprae genomes. The availability of a genome sequence may also be informative in terms of further defining the core gene set of a pathogenic mycobacterium and in retracing the proposed common history with M. leprae [7].
Accession Number and Availability of the Genome Sequence and the Strain
The Mycobacterium leprae 7935681 whole genome shotgun (WGS) project has the project accession LVXE00000000. This version of the project (01) has the accession number LVXE01000000, and consists of sequences LVXE01000001-LVXE01000107.
Acknowledgement
This work is supported and funded by Eurofins Genomics India Pvt Ltd.
References
-
Kim HJ, Brennan PJ, Heaslip D, Mark CU, Robert LM, et al. (2015) Carbohydrate-dependent binding of langerin to SodC, a cell wall glycoprotein of Mycobacterium leprae. Journal of bacteriology 197(3): 615-625.
-
Barker LP (2006) Mycobacterium leprae interactions with the host cell: recent advances. Indian Journal of Medical Research 123(6): 748-759.
-
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data." Bioinformatics 30(15): 2114-2220.
-
Simpson JT, Wong K, Jackman SD, Schein JE, Steven JMJ, et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome research 19(6): 1117- 1123.
-
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4): 578-579.
-
Ramy KA, Bartels D, Best AA, DeJongh M,Terrence D, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC genomics 9(1): 75.
-
Singh P, Cole ST (2011) Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future microbiology 6(1): 57-71.
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