Plant and Animal De novo Sequencing

De novo assembly of plant and animal genomes to enable accurate characterization of complex genomes and species-specific genomic features.

De novo sequencing involves sequencing and assembling the genome of a species without relying on a reference genome, thereby constructing a complete genomic sequence map of the species. This approach not only provides a comprehensive genomic sequence map but also lays the foundation for further research into the species' evolutionary origins and adaptations to specific environments.

With extensive experience in experimental operations and bioinformatics analyses, Novogene offers an accurate, rapid, and comprehensive characterization of species and generates reliable results. Furthermore, Novogene’s end-to-end services guarantee the ultra-fast turnaround time.

Benefits of  Novogene’s Plant and Animal De novo sequencing service

Extensive Experience

Proven expertise in assembling reference-quality genomes for diverse plant and animal species.

High-Quality Data

Delivering high-quality sequencing data with industry-standard performance and assembly-ready contig N50.

Short- and Long-Read Integration

Flexible de novo sequencing strategies combining long-read and short-read data for comprehensive genome assembly.

Advanced Bioinformatics Support

End-to-end assembly solutions from long-read data, with support for T2T genomes and chromosome-level assembly via Hi-C integration.

Customer Service System (CSS)

A centralized platform for project tracking, data access, and seamless collaboration throughout your sequencing workflow.

Applications of Plant and Animal De novo Sequencing

Conservation & Evolutionary Research (Animal)

Uncovers the genetic basis of environmental adaptation, traces evolutionary history, and provides critical insights for protecting endangered species.

Agriculture & Livestock Breeding

Identifies genes associated with disease resistance, productivity, and desirable traits, enabling the development of healthier and higher-yielding breeds.

Biomedical Research & Drug Discovery

Facilitates the creation of better animal disease models (e.g., zebrafish) and aids drug discovery by revealing unique biological pathways from animals with special traits, such as cancer resistance.

Crop Improvement & Food Security (Plant)

Provides the complete genetic blueprint to empower breeding of high-yield, nutrient-rich, and stress-resilient crop varieties, ensuring global food security.

Evolution & Adaptation Studies (Plant)

Reveals evolutionary histories and deciphers the genetic mechanisms behind plant adaptation to environmental challenges.

Genetic Resource Mining

Pioneers the discovery of novel genes responsible for valuable compounds and revolutionary agronomic traits, driving innovation across agriculture and biotechnology.

Applications of Plant and Animal De novo Sequencing

Conservation & Evolutionary Research (Animal)

Uncovers the genetic basis of environmental adaptation, traces evolutionary history, and provides critical insights for protecting endangered species.

Agriculture & Livestock Breeding

Identifies genes associated with disease resistance, productivity, and desirable traits, enabling the development of healthier and higher-yielding breeds.

Biomedical Research & Drug Discovery

Facilitates the creation of better animal disease models (e.g., zebrafish) and aids drug discovery by revealing unique biological pathways from animals with special traits, such as cancer resistance.

Crop Improvement & Food Security (Plant)

Provides the complete genetic blueprint to empower breeding of high-yield, nutrient-rich, and stress-resilient crop varieties, ensuring global food security.

Evolution & Adaptation Studies (Plant)

Reveals evolutionary histories and deciphers the genetic mechanisms behind plant adaptation to environmental challenges.

Genetic Resource Mining

Pioneers the discovery of novel genes responsible for valuable compounds and revolutionary agronomic traits, driving innovation across agriculture and biotechnology.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Platform Type	Sample Type	Amount (Qubit®)	Purity
Illumina NovaSeq System	Genomic DNA	≥ 200 ng	OD260/280=1.8-2.0; no degradation, no contamination
PacBio Revio System	HMW Genomic DNA	≥ 3.5 μg	OD260/280=1.75~2.0; OD260/230=1.5~2.6; *NC/QC=1.00~2.20; Fragments should be ≥30K
Nanopore PromethION	HMW Genomic DNA	≥ 8.5 μg	OD260/280=1.75~2.0; OD260/230=1.4~2.6; *NC/QC=0.95~3.00 Fragments should be ≥30K
Nanopore PromethION (Nanopore Ultra-long DNA Library)	uHMW Genomic DNA	≥ 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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

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	Illumina NovaSeq System	PacBio Revio System	Nanopore PromethION System
Read Length	Paired-end 150 bp	N50>15 kb	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

Project Workflow

Demo Results

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Assembly Statistics

Grain Aphid genome A/T/G/C content statistics

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Assembly Evaluation - BUSCO Assessment

BUSCO assessment results

Note: C: Complete BUSCOs; S: Complete and single-copy BUSCOs; D: Complete Duplicated BUSCOs; F: Fragmented BUSCOs; M: Missing BUSCOs; n: Total BUSCO groups searched

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GC Content and Depth Distribution

X-axis: GC contents; y-axis: sequencing depth.

Upper: GC content distribution.

Lower right: sequencing depth distribution.

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Evidence Support

Venn diagram of gene set evidence support. Augustus, GlimmerHMM, SNAP, Geneid and Genscan are used in De novo gene structure prediction.

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Function Prediction

Venn diagram of gene function annotationProtein sequences predicted by gene structure are aligned with known protein databases. Results suggest that the function of 95.8% of the genes could be predicted.

K-mer Analysis

Kmer=17 analyses and genome size evaluation

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

(1) K-mer: Selected K-mer length.
(2) Depth:The expected value of K-mer depth.
(3) n_K-mer:The total number of K-mer from SOAPdenovo.
(4) Genome size(M):The genome size in Mb estimated by formula: Genome Size=K-mer_num/Peak_depth.
(5) Revise Genome size(M):Revised genome size after error correction from wrong K-mer.
(6) Heteozygous ratio:The percent of heteozygous positions.
(7) Repeat:Calculated by the percentage of K-mer numbers after 1.8-fold of the main peak of total K-mer numbers.
Note: The repeat here is a mathematically repeated sequence but not a repeat element with certain biological functions.

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

K-mer Analysis

Kmer=17 analyses and genome size evaluation

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

Sample	Kmer	Depth	n_kmer	Genome_size(M)	Genome_size(M)	Genome_size(M)	Repeat_rate(%)
plant	17	36	24,079,467,724	668.87	668.87	668.87	73

Frequently Asked Questions

How to Ensure the Reliability of Assembly Results? What Are the Main Methods for Evaluating Assembly Completeness and Accuracy?

In addition to ensuring Contig N50 and Scaffold N50 metrics, it is essential to evaluate the quality of the assembly. Common evaluation methods include BUSCO, LAI, Merqury, CEGMA, EST sequence assessment, RNA sequence assessment, and consensus evaluation. Among these, BUSCO assesses the genome using a library of single-copy orthologous genes, LAI evaluates genome completeness based on long terminal repeat retrotransposons, and Merqury assesses the genome's QV (Quality Value). These three evaluation methods are currently the most widely used.

What is the Recommended Strategy for De Novo Assembly?

Does Survey and Genome De Novo Require the Same DNA?

More Services

Total RNA Sequencing

Full-Length Transcriptome Sequencin

Plant and Animal Whole Genome Sequencing

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Plant and Animal De novo Sequencing

De novo assembly of plant and animal genomes to enable accurate characterization of complex genomes and species-specific genomic features.