GENOMICS

GENOME SEQUENCING (GENOMICS)

Overview – What is the difference between de novo genome sequencing and genome re-sequencing?

Whole-genome sequencing (WGS) is the sequencing of all DNA present in the genome of an organism, including chromosomal DNA, mitochondrial DNA and chloroplast DNA if in plants. Two types of WGS approaches are available that mainly differ in their dependency on a reference genome sequence. 

When a genome is interrogated for the first time, the process of sequencing and genome assembly is called de novo sequencing. In this process, overlapping sequencing reads are assembled into longer fragments that are further pieced together until the entire sequence of the genome is obtained. This method enables genomic characterisation of newly discovered organisms, comparative analysis of highly variable genomes and in-depth exploration of structural variants. 

In cases where a consensus sequence for a specific genome is already available, whole-genome re-sequencing can be applied. In this process, generated reads are directly aligned to the reference sequence. This comparative sequencing enables identification of single-nucleotide polymorphisms (SNPs), insertions-deletions (InDels) and structural variations between organisms. The detailed genetic background of an individual is relevant for fields like plant and animal breeding, population genetics and clinical applications such as determining disease risk factors and discovering novel biomarkers for diseases diagnosis. 

Applications – What are the advantages of genome re-sequencing and de novo genome sequencing?

Re-sequencing is particularly useful for:

  • Comparing variations across multiple genomes
  • Characterising variations like SNPs and InDels
  • Detecting large structural variants like duplications, inversions, genomic rearrangements, copy number variations (CNV) 
  • Updating reference genome with newly identified mutations
  • Genotyping
  • Exploring genetic evolution
  • Performing Genome Wide Association Studies (GWAS)

De novo sequencing enables:

  • Studies of the genetic make-up of newly discovered organisms
  • Comparative analysis of genomes that are highly variable
  • In-depth variant characterisation

Scientific expertise: genome re-sequencing and genome assembly

Extra-long sequencing reads are extremely beneficial for obtaining complete genome assemblies. The company performs de novo genome sequencing on the PacBio platform, which generates the industry’s longest sequencing reads. This enables gap closure and finishing of genomes. GATC Biotech also realises the importance of accuracy in genome sequencing. The company provides the option of using shorter reads with lower error rates generated on Illumina platforms. For de novo genome sequencing or re-sequencing purposes, data from the two platforms can be combined or analysed separately to provide quality novel and re-sequenced genomes. 

Publications

Find here, a list of selected research articles supported by GATC Biotech ’s sequencing products, as well as the latest publications on de novo genome sequencing and re-sequencing.

Products related to de novo genome sequencing and genome re-sequencing

Do you want to be the first to sequence the genome of your organism of interest? Guaranteed results with fast turnaround times are now available with our INVIEW DE NOVO GENOME standardised service.  

Does the reference genome sequence of your model organism already exist? Then perform comparative analysis with our whole-genome re-sequencing or targeted sequencing services and benefit from the combination of library preparation, sequencing and expert BioIT analysis to obtain top-quality sequencing data. 

Further reading on genome sequencing

Sanchez-Flores, A., Abreu-Goodger, C. A practical guide to sequencing genomes and transcriptomes. Curr Top Med Chem. 14(3), 398 – 406 (2014).

Bentley, D.R. Whole-genome re-sequencing. Curr Opin Genet Dev. 16(6), 545 – 552 (2006).