Sample Submission GuidelinesWhat Is De Novo Whole Genome Sequencing
De novo sequencing, also known as whole-genome sequencing, refers to the process of sequencing an organism without any prior reference sequence information. Through bioinformatics analysis methods such as assembly and alignment, the genomic sequence of the species can be obtained. By using whole-genome de novo sequencing technology, the complete genomic sequences of animals, plants, bacteria, and fungi can be obtained, thereby advancing the research of these species. Once the whole-genome sequence is completed, a genomic database for the species can be constructed, providing an efficient platform for post-genomic studies of the species and supplying DNA sequence information for subsequent gene mining and functional validation. With the use of next-generation high-throughput sequencing technologies, it is possible to efficiently and cost-effectively obtain the genomic sequences of all species, including animals, plants, bacteria, and fungi, thereby promoting research on these species.
Our De Novo Whole Genome Sequencing Service
CD Genomic offers a one-stop solution for de novo genome sequencing services, covering experimental design, sample preparation, sequencing, and bioinformatics analysis, aiming to provide genomic solutions for your research. Our de novo genome sequencing services include:
De novo sequencing of animal and plant genomes.
De novo sequencing of bacterial genomes.
De novo sequencing of fungal genomes.
De novo sequencing of metagenomes.
Our De Novo Whole Genome Sequencing Service Advantages
Platform Advantages: Obtaining high-quality genomic maps
High-depth sequencing: High accuracy Rich data analysis content:
Standard analysis, advanced analysis, customized analysis Extensive experience in genome sequencing and analysis:
Successfully completed numerous large-scale genome sequencing projects
Customized genome sequencing solutions: Personalized genome sequencing solutions can be tailored according to specific requirements.
De Novo Whole Genome Sequencing Workflow
Bioinformatics Analysis
I. Data analysis for animal and plant de novo genome sequencing
II. Data analysis for bacterial and fungal de novo genome sequencing
Sequencing Platform and Strategy
Illumina HiSeq X Ten, PacBio SMRT, or Oxford Nanopore.
Depth of coverage ≥ 100x.
More than 80% of bases with a ≥Q30 quality score.
Both paired-end library and mate-pair library can be constructed in the library preparation step.
Sample Requirements
| Service | Sample Type | Recommended Quantity | Minimum Quantity | Minimum Concentration |
| Whole Genome Sequencing (Illumina) | Genomic DNA | ≥ 500 ng | 200 ng | 10 ng/µL |
| Whole Genome Sequencing (PCR-free) | Genomic DNA | ≥ 1 µg | 500 ng | 20 ng/µL |
| Whole Genome Sequencing (PacBio) | Genomic DNA | ≥ 3 µg | 80 ng/µL | |
| Whole Genome Sequencing (Nanopore) | Genomic DNA | ≥ 5 µg | 20 ng/µL |
1.Comparative Genomic Analysis
Using the progressiveMauve software, the chromosome sequences of 9 strains of Escherichia coli O104:H4 isolates are aligned to show information on mobile genetic elements and genomic variable regions. By utilizing the core SNP (Single Nucleotide Polymorphism) site information, a maximum likelihood phylogenetic tree is constructed to reveal the evolutionary relationship among the strains.
(Grad, Yonatan H., et al., 2013)
2. Repeat Sequence Analysis
Two methods, de novo prediction and database-based alignment, are employed to analyze the transposable elements (TEs) in the genome sequences of the Natal longhorned beetle and the Dampwood termite. The results from both methods are integrated and analyzed using the RepeatModeler software to construct a transposable element sequence database. The RepeatClassifier software is used to classify the transposable elements. The sequence variation rate of transposable elements in both termite genomes is calculated to reveal potential mechanisms of genome expansion.
(Korb,Judith, et al., 2015)
3. Metabolic Pathway
Reconstruction Based on the genome annotation information of the restriction-free dechlorinating bacterium (PER-K23), the biosynthesis of quinoline-like compounds is predicted to involve four metabolic pathways.
(Rupakula, Aamani,et al., 2014)
4. Gene Evolution Analysis
Using the gene sequences of 117 single-copy orthologous proteins, a maximum likelihood species phylogenetic tree is constructed for the strains of Mollicutes, Haloplasma, and Firmicutes. This analysis reveals the acquisition and loss of the mreB and fib genes in the genomes of different bacterial strains.
(Ku, Chuan, Wen-Sui Lo, and Chih-HorngKuo., 2014)
