De Novo Whole Genome Sequencing Service

What is De Novo Whole Genome Sequencing

Whole-genome de novo sequencing, also known as de novo sequencing, enables the sequencing of a species without relying on any pre-existing genetic sequence information. Through bioinformatic methods, the obtained sequences are assembled and aligned, resulting in a detailed genomic map of the species under study. This approach facilitates the acquisition of entire genomic sequences for a diverse array of organisms, including animals, plants, bacteria, and fungi, thereby propelling forward our understanding and research of these species.

Upon finalizing the whole-genome sequencing process, a comprehensive genomic database can be established for the species in question. This database serves as a robust platform for subsequent post-genomic studies, enhancing the capability to undertake gene mining and functional validation work effectively. The advent and application of next-generation high-throughput sequencing technologies have rendered it feasible to procure the genomic sequences of various organisms in a manner that is both cost-effective and efficient. Consequently, these advancements are significantly driving research and expanding our knowledge base across the biological sciences, encompassing animals, plants, bacteria, and fungi.

Overall, employing whole-genome de novo sequencing techniques enables the acquisition of complete genomic sequences of various organisms, such as plants and animals, thus stimulating subsequent research endeavors pertaining to these species. Upon completion of the whole-genome sequencing, a comprehensive genomic database can be established for the species in question. This database serves as an efficient platform for post-genomic studies, facilitating gene discovery and functional verification by providing critical DNA sequence information.

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.

Advantages of Our De Novo Whole Genome Sequencing Service

• 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.

Application of De Novo Whole Genome Sequencing

• Obtaining the reference sequence of a species
• Studying the origin and evolutionary history of a species
• Mining functional genes
• Establishing a species database
• Research on the genome of a new species
• Analysis of complex genome structures
• Population genetics and genomic diversity
• Disease genomics
• Functional genomics and regulatory elements

Workflow of De Novo Whole Genome Sequencing

Our De Novo Whole Genome Sequencing Service starts with DNA extraction, followed by state-of-the-art sequencing and rigorous bioinformatics analysis. We provide accurate genome assembly and annotation to uncover genetic insights effectively.

Service Specifications

	Sample Requirements Whole Genome Sequencing: Genomic DNA ≥ 500 ng Minimum Quantity: 200 ng Concentration≥ 10 ng/µL Whole Genome Sequencing (PCR-free): Genomic DNA ≥ 1 µg Minimum Quantity: 500 ng Concentration≥ 20 ng/µL Whole Genome Sequencing (PacBio) Genomic DNA ≥ 1 µg Concentration≥ 80 ng/µL Whole Genome Sequencing (Nanopore) Genomic DNA ≥ 5 µg Concentration≥ 20 ng/µL OD260/280=1.8~2.0 All DNA samples are validated for purity and quantity. Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
Click	Sequencing 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.
	Bioinformatics Analysis Genome survey Genome size estimation Heterozygosity estimation Repeat sequence estimation Genome pre-assembly Assembly quality assessment Genome annotation Gene family clustering Evolutionary analysis Structural and functional studies Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Analysis Pipeline

I. Data analysis for animal and plant de novo genome sequencing

II. Data analysis for bacterial and fungal de novo genome sequencing

Deliverables

• The original sequencing data
• Experimental results
• Data analysis report
• Details in De Novo Whole Genome Sequencing for your writing (customization)

Partial results are shown below:

1. What is the difference between de novo and reference assembly?

De novo assembly involves constructing a genome sequence from scratch without relying on a pre-existing reference genome, which is particularly useful for species without a known genome sequence. Reference assembly, on the other hand, uses an existing genome sequence as a template to align and map sequencing reads, allowing for the identification of genetic variations in the studied genome relative to the reference.

2. How to assess the quality of genome de novo assembly?

The quality of genome de novo assembly is commonly evaluated using metrics such as contig N50 and scaffold N50. The N50 value is determined by arranging the assembled contigs or scaffolds from largest to smallest and identifying the length of the contig or scaffold at the point where the cumulative length surpasses 50% of the total assembly length. This value provides significant insight into the continuity and completeness of the assembled sequences. Additional measures like N70 and N90 are calculated similarly, with the percentage thresholds adjusted to 70% and 90%, respectively. These metrics collectively serve to comprehensively evaluate the integrity and reliability of the genome assembly.

3. Is the DNA used in survey sequencing and whole-genome de novo sequencing required to be the same?

In principle, the DNA used for both survey sequencing and de novo sequencing should originate from the same individual. If the amount of DNA is insufficient for the entire de novo sequencing project, it is recommended that the DNA for the short-read library comes from the same individual. For third-generation sequencing long-read or even ultra-long-read libraries, DNA from another individual within the same population may be used.

Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Journal: Advanced Science

Impact factor: 15.804

Published: 28 November 2019

Background

Peanut is a vital global oilseed legume, originating from South America and cultivated predominantly in Asia and Africa. Its evolution from wild diploid species to cultivated tetraploid forms offers insights into polyploid genome evolution and crop domestication, crucial for enhancing global food and oil security. The authors utilized genome sequencing and comprehensive genomic analysis to study the evolution and domestication of peanuts.

Materials & Methods

Results

The study resequenced genomes of 17 wild diploids and 30 wild/cultivated tetraploids, performing phylogenetic and PCA analyses to classify them into wild and cultivated groups. It showed that cultivated tetraploids evolved from wild tetraploids. A whole genome duplication occurred ≈58 million years ago, accelerating sequence divergence in tetraploid peanuts. The study reconstructed the evolution of allotetraploid peanuts, highlighting hybridization and domestication events around 4500 years ago, impacting agronomic traits and resistance characteristics.

Fig 1. Subgenome origins and phylogenetic analysis of wild and cultivated peanut lines.

In tetraploid peanuts, asymmetric evolution between subgenomes was evident. Sequence exchanges favored A to B subgenomes, influencing gene family sizes and pathways like flavonoid biosynthesis. Expression bias during pod development indicated divergent roles of A and B subgenomes. Selection pressures differed between wild and cultivated forms, highlighting asymmetric impacts on gene evolution and expression in peanuts.

Fig 2. Asymmetric subgenome evolution of allotetraploid peanuts.

SVs (deletions and insertions) influence gene expression and traits in peanuts.Analysis of homoeologous pairs reveals different selection pressures on SV genes between subgenomes during peanut domestication, indicating distinct patterns of SV accumulation and evolutionary impacts.

Fig 3. Asymmetric SV accumulation from wild diploids to allotetraploid peanuts.

Conclusion

The high-quality sequence of wild tetraploid peanut bridges the genomic gap between diploid and cultivated species, revealing asymmetric evolution in subgenomes and providing valuable resources for studying polyploid evolution and peanut improvement.

Reference

1. Yin D, Ji C, Song Q, Zhang W, Zhang X, Zhao K, Chen CY, Wang C, He G, Liang Z, Ma X. Comparison of Arachis monticola with diploid and cultivated tetraploid genomes reveals asymmetric subgenome evolution and improvement of peanut. Advanced Science. 2020, 7(4):1901672.