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A team of researchers from Rutgers University updated the reference sequence for Mycobacterium tuberculosis strain H37Rv in a recent publication in Nature Communications.
The previous reference sequence for M. tuberculosis, the causative agent of tuberculosis, was commonly used in research despite containing inaccuracies. Tuberculosis is a leading cause of death worldwide and causes illness for millions of people each year (World Health Organization). Therefore, the availability of an accurate reference genome was crucial for clinical and infectious disease research.
Assembly of a complete M. tuberculosis genome was challenging due to the organism’s highly repetitive regions, which account for around 10% of the genome. These difficult regions also make an assembly using short reads much more difficult. To combat these challenges, the researchers used the MinION from Oxford Nanopore to obtain the needed long reads and polished the assembly using short reads from Illumina instruments.
The final assembly of strain H37Rv added 6.4 kb of new sequence into the reference along with changes to 10 major regions. It also led to the development of Bact-Builder, a new tool for de novo assembly of accurate bacterial genomes.
Bact-Builder uses long reads for a consensus-based assembly and further polishes the assembly with both long and short reads. It was first designed using reads generated in silico and was then tested using actual reads from the MinION and Illumina’s NovaSeq.
The creation of Bact-Builder can help researchers build other bacterial genomes and the changes to the H37Rv reference sequence hope to improve tuberculosis research worldwide.
Read the original journal article here.
The previous reference sequence for M. tuberculosis, the causative agent of tuberculosis, was commonly used in research despite containing inaccuracies. Tuberculosis is a leading cause of death worldwide and causes illness for millions of people each year (World Health Organization). Therefore, the availability of an accurate reference genome was crucial for clinical and infectious disease research.
Assembly of a complete M. tuberculosis genome was challenging due to the organism’s highly repetitive regions, which account for around 10% of the genome. These difficult regions also make an assembly using short reads much more difficult. To combat these challenges, the researchers used the MinION from Oxford Nanopore to obtain the needed long reads and polished the assembly using short reads from Illumina instruments.
The final assembly of strain H37Rv added 6.4 kb of new sequence into the reference along with changes to 10 major regions. It also led to the development of Bact-Builder, a new tool for de novo assembly of accurate bacterial genomes.
Bact-Builder uses long reads for a consensus-based assembly and further polishes the assembly with both long and short reads. It was first designed using reads generated in silico and was then tested using actual reads from the MinION and Illumina’s NovaSeq.
The creation of Bact-Builder can help researchers build other bacterial genomes and the changes to the H37Rv reference sequence hope to improve tuberculosis research worldwide.
Read the original journal article here.