Abstract
ABSTRACTThis report describes the genome sequences of two Mycobacterium tuberculosis isolates, S1 and S3, recovered from Asian elephants in Nepal. These genome sequences will enhance our understanding of the genomic epidemiology of Mycobacterium tuberculosis in Asian elephants.
Highlights
Asian elephants (Elephas maximus) are an endangered species (1) with fewer than 50,000 individuals remaining worldwide (2)
The reads were analyzed using Kraken[2] v2.1.2 to eliminate contaminating sequences (5), and 92.7% of S1 and 99.12% of S3 reads were mapped to the Mycobacterium tuberculosis complex (MTBC) using the Kraken[2] default parameters and database
HISAT2 v2.2.1 was used to determine the coverage of reads relative to M. tuberculosis H37Rv (GenBank accession number NC_000962.3) (6)
Summary
Asian elephants (Elephas maximus) are an endangered species (1) with fewer than 50,000 individuals remaining worldwide (2). The NEBNext DNA library prep kit (New England BioLabs, Ipswich, MA) was used to generate paired-end (2 Â 150-bp) libraries, which were quality checked using Qubit 2.0, the Agilent 2100 Bioanalyzer, and quantitative PCR (qPCR) prior to whole-genome sequencing (WGS) on the Illumina NovaSeq 6000 platform. Novogene’s custom software trimmed adapters and discarded paired-end reads containing contaminant adapter sequences, pairs of reads containing more than 10% uncertain nucleotide calls, and pairs containing Phred scores less than or equal to 5. The reads were analyzed using Kraken[2] v2.1.2 to eliminate contaminating sequences (5), and 92.7% of S1 and 99.12% of S3 reads were mapped to the Mycobacterium tuberculosis complex (MTBC) using the Kraken[2] default parameters and database.
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