Plant and Animal de novo Sequencing

Plant and Animal De novo Sequencing

Reference-free genome assembly for plant and animal species, supporting genome structure, species evolution and trait-related research.

For many plant and animal species, especially non-model organisms, a high-quality reference genome may be limited or unavailable. De novo sequencing helps researchers build new genome assemblies from sequencing data, supporting studies of genome structure, species evolution, adaptation and trait-related biology.

Novogene Europe supports plant and animal de novo sequencing projects with short-read, long-read and chromosome-level assembly strategies. Bioinformatics workflows can support genome assembly, annotation and comparative analysis, helping researchers develop reliable genome resources for downstream research.

Service Highlights

Reference Genome Construction

Build new genome assemblies for plant and animal species where a suitable reference genome is limited, incomplete or unavailable for analysis.

Long-read Assembly Options

Long-read and ultra-long sequencing options support high-contiguity assembly for complex plant and animal genomes with repetitive or variable regions.

Chromosome-level Assembly

Hi-C-based assembly strategies can support chromosome-level genome construction and improve genome structure resolution across larger or more complex genomes.

Annotation and Comparative Analysis

Bioinformatics workflows support genome annotation, functional interpretation and comparative analysis to help develop genome resources for downstream biological research.

Applications

Evolution and Adaptation

Plant and animal de novo sequencing helps researchers investigate genome evolution, species differentiation and genetic mechanisms linked to environmental adaptation.

Breeding and Trait Research

New genome assemblies can support identification of genes and genomic regions associated with important agricultural, productivity, resistance or quality-related traits.

Conservation Genomics

Reference genome resources can support studies of endangered or non-model species, helping researchers explore genetic diversity, population history and conservation-relevant biology.

Comparative Genomics

De novo assemblies provide genome resources for comparing species, lineages or related organisms to investigate genome structure, gene content and species-specific features.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Platform Type	Sample Type	Amount (Qubit®)	Purity
IlluminaNovaSeq X Plus /NovaSeq6000	Genomic DNA	≥ 100 ng	OD260/280=1.8-2.0;no degradation, no contamination
	Genomic DNA(PCR free customized)	≥ 2 μg
	Genomic DNA(PCR free)	≥ 1.2 μg
PacBio Revio DNA HiFi library	HMW Genomic DNA	≥ 3 μg	OD260/280=1.75-2.0; OD260/230=1.5-2.6; *NC/QC=1.0-2.2Fragments should be ≥ 30 kb
Nanopore PromethION DNA library	HMW Genomic DNA	≥ 8 μg	OD260/280=1.75-2.0; OD260/230=1.4-2.6; *NC/QC=0.95~3.00Fragments should be ≥ 30 kb
Nanopore Ultra-long DNA Library	uHMW Genomic DNA (plant and animal tissues）	≥ 20 μg	OD260/280=1.7-2.0; OD260/230=1.3-2.6; *NC/QC=0.95-3.00; Fragments should be ≥ 100k, no fragments below 30k.

*NC/QC = NanoDrop concentration/Qubit concentration

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Type	Short-read Sequencing	PacBio Revio	Nanopore PromethION
Read Length	Paired-end 150 bp	N50>15 kb, long read lengths up to 25 kb（CCS）	average > 50 kb
Recommended Sequencing Depth	For genome survey or assembly polishing: ≥ 50× RNA requires 4 to 6 different tissue sites.	For genome assembly: ≥ 30×
Standard Analysis	K-mer analysis GC content analysis Repeat content rate evaluation Heterozygous rate evaluation Genome size evaluation	Long-read assembly Assembly statistics Gene completeness evaluation
Genome Annotation	－	Repeat prediction Structure prediction Function prediction Noncoding RNA prediction

Resources

Example Analysis Output

1/1

Assembly Quality

Assess genome assembly completeness using BUSCO single-copy orthologues to evaluate gene content recovery.

1/1

Repeat Divergence Analysis

Visualise repeat sequence divergence to explore repeat composition, activity and genome evolution patterns.

1/1

Functional Annotation Overlap

Summarise overlap of predicted gene annotations across databases to support genome function interpretation.

Webinars

Getting Started with Genomics: Next Generation Sequencing Essentials for 2024

Discover the fundamentals of Next-Generation Sequencing (NGS) and learn how leading technologies such as Illumina, PacBio, and Oxford Nanopore are advancing genomic research and unlocking new possibilities in DNA analysis.

Learn More

Frequently Asked Questions

How is assembly reliability evaluated?

Researchers assess assembly reliability using continuity, completeness, and accuracy metrics such as contig N50 and Scaffold N50.

Common evaluation methods include BUSCO, LAI, Merqury, CEGMA, EST sequence assessment, and consensus evaluation. BUSCO assesses the genome using a library of single-copy orthologous genes. LAI measures the structural completeness of repetitive, structural parts of the genome. Merqury evaluates assembly consensus quality and completeness using high-accuracy k-mer profiles derived from sequencing reads.

What is the recommended strategy for de novo genome assembly?

Can de novo assemblies identify structural variants and repeats?

Can de novo genome assemblies support downstream functional studies?

Explore Genomics Insights

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

Speak with a Specialist

Have a project in mind?

Send us your enquiry and a Novogene Europe specialist will be in touch.