De novo sequencing refers to sequencing the genome of a species without any reference genome information, and using bioinformatics analysis methods to splice and assemble the genome sequence map of the species to advance the subsequent research of the species.

CD Genomics has the professional technical team with extensive experience in experimental operations and bioinformatics analysis. We provide accurate, efficient, comprehensive and complete species characterization to ensure reliable experimental results.We provide de novo sequencing of plants and animals, mainly for plant and animal species with unknown genome sequences or poorly assembled reference genomes, by constructing different types of genomic DNA libraries and performing sequence determination and bioinformatics analysis to help our clients map the complete genome sequence information of the species.

Applications of animal and plant de novo sequencing

• Provide a theoretical basis for agricultural genetic variation research.
• Guiding animal health and screening excellent breeds.
• Screening new plant varieties.
• Guiding drug screening.
• Explore the relationship between species origin and evolution.
• Provide new insights into patterns of genomic variation.
• Genome + Population Evolution: Unraveling the origin and evolution of species, as well as mechanisms for environmental adaptation.
• Genome + Transcriptome + Metabolome: Deciphering the synthesis pathways of key metabolites.
• Genome + Comparative Genomics: Determining species classification and evolutionary history.
• Genome + Gene Mapping (GWAS/QTL): Locating crucial genes and understanding the mechanisms behind the formation of significant traits in a species.
• Pan-Genomics: Analyzing structural variations, genetic differences, and species adaptability within populations.

DNA sample requirements

Plant and animal de novo sequencing workflow

From obtaining the sample genomic DNA, checking the quality of the sample genomic DNA, to constructing a library of genomic DNA that meets the requirements, and dividing the library into small fragment library and large fragment library according to the fragment size, and checking the library quality of the constructed library, to analyzing the sequencing data, data quality control, and bioinformatics analysis. Each step is carefully controlled and scientifically designed to ensure the correct results.

Fig 1. De novo sequencing workflow

Choose your de novo sequencing plan

• Next-Generation Sequencing: Utilizing the data from NGS platforms, a genome survey is conducted to determine genome size, heterozygosity, and repetitive sequences. This approach provides insights into genome complexity, with a recommended sequencing data volume of 100X.
• Long-read Sequencing: Leveraging data from long-read sequencing platforms, genome assembly is performed to generate assembly fragments (contigs). Specific recommendations for various platforms are as follows: PacBio HiFi data is recommended at 30X-50X, PacBio CLR data at 100X, while Nanopore data is not recommended due to its lower accuracy, but if used, a sequencing data volume of 100X is suggested.
• Hi-C Sequencing: This method leverages the three-dimensional spatial structure of chromatin. Genomic fragment segments (contigs) assembled from long-read sequencing data are mapped onto chromosomes to achieve chromosome-level genome assembly. A recommended sequencing data volume is typically 100X.
• ONT Ultra-Long (Ultra-Long ONT): Featuring extended read lengths, this technology is employed to bridge genome gaps, achieving telomere-to-telomere zero-gap level genomes. Notably, T2T genomes for watermelon, Arabidopsis thaliana, rice, maize, and other species have been successfully constructed, signaling the advent of T2T genomes (level 4.0). A suggested sequencing data volume is around 50X.

Our advantages and features

• Experience. CD Genimics has extensive experience in plant and animal de novo sequencing services and is recognized by industry professionals worldwide.
• Expertise. CD Genimics has the latest mass spectrometry instruments and analysis software, and integrates sequencing results from various sequencing platforms to provide expert services for de novo sequencing.
• Time-saving and efficient. CD Genimics delivers your results in the shortest possible time, saving your research time.
• Reliable results. Our technical team delivers the most reliable results for your experiments.

CD Genomics offers a full suite of state-of-the-art sequencing equipment and software, high-quality sequencing reagents and industry-leading data quality, as well as integrated workflows that streamline de novo sequencing from library preparation to data analysis, ensuring our customers get the fastest and most accurate results while helping them save more time on their research and ensuring a high turnaround on their experiments. If you are interested in us, please feel free to contact us.

FAQ

How do I decide between genome resequencing and de novo sequencing?

(1) When dealing with a species lacking a reference genome, de novo sequencing is necessary to assemble the genome from scratch.

(2) If a species possesses an incomplete reference genome, opting for de novo sequencing becomes essential to assemble a more comprehensive genome.

(3) In cases where a single reference genome falls short of capturing all the genetic information within a species, de novo sequencing is required to assemble a pan-genome that encompasses greater genetic diversity.

What sets apart a genomic framework map from a fine map?

A framework map provides comprehensive coverage, encompassing 90% of the autosomal genome and 95% of the gene region. It specifies Contig N5 to 5 kb, Scaffold N50 up to 20 kb, and maintains a remarkable single-base error rate of less than 1 in 100,000.

On the other hand, a fine map exhibits even greater precision, covering 95% of the autosomal genome and an impressive 98% of the gene region. It delineates Contig N5 to 20 kb, and Scaffold N50 up to 300 kb, with a single-base error rate consistently below 1 in 100,000. This nuanced contrast highlights the enhanced resolution and detailed information offered by a fine map compared to a genomic framework map.

Why construct diverse libraries for sequencing plant and animal genomes?

The complexity and size of these genomes, with numerous repetitive regions, necessitate specialized gradient sequencing libraries. This approach, combined with BAC or Fosmid libraries and multiple sequencing platforms, ensures accurate and comprehensive mapping, avoiding mis-splicing caused by repetitive sequences and enhancing overall genome integrity in higher plants and animals.

What sequencing platforms do you offer in animal and plant de novo sequencing service?

CD Genomics offers a comprehensive range of sequencing platforms, including Illumina, Nanopore and PacBio SMRT Sequencing.

The Illumina platform excels in its cost-effectiveness and large sequencing data volume, providing high coverage for genome sequencing. However, its short read lengths and GC preferences pose challenges in navigating repetitive and GC-rich regions. Sequencing data volumes of 100X are generally recommended.

Our long-read sequencing platforms, PacBio RS II and Sequel, stand out with long reads (average length > 10 kb), rapid sequencing (2-6 hours for a single SMRT cell), high throughput (averaging ~8G of valid data per SMRT cell), absence of GC preference, and the ability to detect base modification information, including methylation. This makes them especially well-suited for the comprehensive sequencing of plant and animal genomes from scratch. PacBio HiFi data, 30X~50X (recommended); PacBio CLR data, recommended 100X.