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Whole genome sequencing is a technique used increasingly in taxonomy. The genomic sequence of a strain (complete or draft) makes it possible to study and characterize the microorganism by genomic analysis (gene annotation, detection of genomic islands, etc.). It also allows phenotypic inference studies to establish correspondence between the genome sequences observed and phenotypic characteristics of the strain.

In addition, genome sequencing can provide useful genomic data for taxonomy, such as the Average Nucleotide Identity (ANI) or estimated DNA-DNA hybridization (eDDH) in silico.

Necessary material

Preferably, an active culture of the strain (petri dish or agar slant).

If the customer prefers, we can also work with genomic DNA of the strain. In that case, the genomic DNA must be delivered in cold-storage and be of good quality (A260 / A280 between 1.8 and 2). We require more than 2 micrograms of DNA at a concentration of 40 ng/µl resuspended in ultrapure water or in TE buffer.

Methodology

At the CECT, full genome sequencing is performed by massive sequencing (NGS) using the Illumina MiSeq platform.

Depending on the number of strains to be sequenced and the genome size of each, costs can be optimized (see fees).

The customer receives the files obtained with raw sequences.

Subsequent analysis (assembly, annotation, index calculation) is not included in the sequencing service but can be ordered separately.

 
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