De novo Sequencing

De novo sequencing aims to sequence a species afresh from the beginning without referencing any previous sequencing data of the species. Decoding the whole genome sequence is one of the most effective methods to understand a species. Based on the genome characteristics, two different strategies are used to obtain the whole genome map.

Workflow

Table 1 Genome Characteristics for common and complex genomes

*All conditions need to be met      **Only one of these conditions need to be met

Strategy for Common Genomes

Strategy for Complex Genomes

Figure 1. Technology Pipeline for de novo Sequencing

Applications

• Mining gene resources
• Finding functional genes
• Facilitating molecular breeding
• Supporting evolution analysis

Advantages

• The leading level of constructing different gradient insert libraries to ensure the assembly crossing many different repeats and generate whole genome map
• Excellent genome assembly by BGI’s indenpendently developed assembly software-SOAPdenovo
• The NGS high throughput sequencing platforms remarkably reduced the cost and only take 6 months to complete a genome project
• The most powerful and experienced bioinformatics team that has completed Rice, Silkworm, Cucumber, Giant Panda and Ant genome projects, etc

Bioinformatics Analysis

• Genome analysis: Genome size, GC content, heterozygous rate, repeat content, sequence depth, autosomal and gene region coverage evaluation.
• Genome annotation: Repeat sequence, ncRNA annotation, gene prediction, gene function annotation.
• Comparative genomics and evolution analysis: Orthologous gene clusters, phylogenetic analysis, whole genome alignment, segmental duplication, conserved element.

Sequencing to reveal evolutionary process

De novo sequencing enables you to study genomes within the same species (Species Pan Genomes) or decode genomes in the same family or genus (Clade Genomes). See Figure 6 for evolution research based on de novo sequencing.

Bioinformatics analysis for species pan genomes and clade genomes:

• 1. Predict genomic functional elements and obtain differentiation characteristics
• 2. Detect gene family expansion or contraction and the birth or death of genes
• 3. Construct gene relationships
• 4. Analyze natural selection and biological adaptation
• 5. Reveal species divergence mechanism and progress
• 6. Detect genomic variation between species (InDels, duplication, retrotransposons)