Please select your location below for region-specific information.
Americas

(North America, South America, and the Caribbean)

Asia-Pacific

(Including Hong Kong SAR, Macau SAR, and Taiwan)

EuropeMainland China
EuropeMainland China
Middle-East & AfricaJapan
JapanKorea
KoreaMiddle-East & Africa
Power your research with expert solutions and reliable results.
Research Services

Animal and Plant De novo Sequencing

Introduction to Animal and Plant De novo Sequencing

De novo sequencing is the process of sequencing a genome without the use of a reference genome and this can be applied to both plant and animal species that do not yet have a reference quality genome. This approach involves assembling a reference genome by piecing together sequencing reads to construct the entire genome sequence. Animal and Plant de novo sequencing is valuable in fields such as evolutionary biology, agriculture, demographic studies, and mutagenesis studies.

Novogene has extensive experience with Animal and Plant de novo sequencing with a diverse range of species. We provide PAWGS de novo sequencing service using long read sequencing strategies, complemented by short read sequencing data for purposes of genomic survey. Our service is complete with high-quality data, bioinformatics support to assist with genome assembly analysis and “publication-ready“ figures accompanying the analysis.

Applications of Animal and Plant De novo Sequencing

Animal and Plant de novo sequencing has applications in several fields such as:

  • Evolutionary biology  
  • Agriculture research 
  • Animal breeding research 
  • Drug screening studies 
  • Developmental biology 
  • Veterinary medicine 

If you are instead interested in applications requiring resequencing of plant and animal species, please refer here. 

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

  • Extensive Experience: Novogene has extensive experience with assembling reference quality genomes for a wide range of plant and animal species using Animal and Plant de novo sequencing.  
  • High-Quality Data: We deliver high-quality sequencing data that meets leading industry standards and contig N50 lengths appropriate for genome assembly.  
  • Short Read and Long Read Sequencing: Novogene offers you with the option of carrying out de novo sequencing of plant and animal samples with long read sequencing strategies, complemented by short read data for purposes of genomic survey.  
  • Bioinformatics Support: We provide comprehensive bioinformatics support to generate de novo assembled reference genomes using long read sequencing data complemented by short read sequencing data. Ultra-long ONT sequencing data can be used to generate telomere-to-telomere (T2T) zero-gap level genomes. Supplementing de novo analysis with Hi-C sequencing data from pre-made libraries can be leveraged to obtain chromosome-level genome assembly. 
  • Fast Turnaround Times: Our sequencing labs are located near you, in Germany and the UK, allowing for reduced shipping times. With our large sequencing capacity, automated and streamlined workflows, we ensure that you receive your data promptly without compromising on data quality. 
  • Customer Service System (CSS): Novogene’s Customer Self Service System (CSS) is an online project management portal that streamlines project management and provides direct access to all your sequencing projects in one place. You can view your sequencing project(s), track their progress, access reports, collaborate with your team members, and obtain other useful information at one place. 

Animal and Plant De novo Sequencing Specifications: DNA Sample Requirements

Illumina

Service Sample Type Amount (Qubit®) Volume Concentration Purity(NanoDrop™/Agarose Gel)
Plant & Animal de novo sequencing(350 bp insert size) Genomic DNA ≥100 ng ≥20 μL ≥5 ng/μL OD260/280 = 1.8-2.0;
no degradation, no
contamination
Fragments longer than 1000 bp
PCR-freePlant & Animal de novo sequencing(350 bp insert size) Genomic DNA ≥1.2 μg ≥20 μL ≥20 ng/μL OD260/280 = 1.8-2.0;
no degradation, no
contamination
PCR-freePlant & Animal de novo sequencing(custom size, ≤500 bp) Genomic DNA ≥2 μg ≥20 μL ≥30 ng/μL

PacBio

Service Sample Type Amount (Qubit®) Volume Concentration Purity
PacBio DNA HiFi library HMW* genomic DNA (Plant & Animal) ≥5 μg ≥50 μL ≥70 ng/μL OD260/280=1.75~2.0;
OD260/230=1.5~2.6;
NC/QC* =1.00~2.20
Fragments should be ≥30K

*HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

ONT

Service Sample Type Amount (Qubit®) Volume Concentration Purity
Nanopore PromethION DNA library HMW* genomic DNA (Plant & Animal) ≥8 μg ≥50 μL ≥100 ng/μL OD260/280=1.75~2.0;
OD260/230=1.4~2.6;
NC/QC*=0.95~3.00
Fragments should be ≥30K

*HMW = High Molecular Weight; NC/QC = NanoDrop concentration/Qubit concentration

Novogene Workflow of Animal and Plant De novo Service

From sample preparation library preparation, short and long-read sequencing, and data quality control, to bioinformatics analysis, Novogene provides high-quality products and professional services. Each step is performed in agreement with a high scientific standard and meticulous design to ensure high-quality research results.



Featured Publications of Animal and Plant De novo Sequencing

Long Read Sequencing

Assembly statistics


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

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

Assembly evaluation- CEGMA assessment


Sequencing depth distribution

Note:
X-axis: sequencing depth/X; y-axis, proportion of bases in the genome

 


GC content and depth distribution

Note:
X-axis: GC contents; y-axis: sequencing depth.
Upper: GC content distribution. Lower right: sequencing depth distribution.

Genome Annotation

Structure prediction

Augustus, GlimmerHMM, SNAP, Geneid and Genscan are used in De novo gene structure prediction.

 

Venn diagram of gene set evidence support

Function prediction

Protein 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.

 


Venn diagram of gene function annotation

Short Read Sequencing

K-mer Analysis

Kmer=17analyses and genome size evaluation

Kmer Depth n_kmer Genome_size(M) Revised Genome_size(M) Heterozygous_rate(%) Repeat_rate(%)
17 67 203,660,880,738 3,039.71 3,020.12 0.46 60.41

Note:
(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.


Distribution of K-mer number/type frequency and depth

Note：
X-coordinate is K-mer depth. Y-coordinate is the frequency of each K-mer depth.

 

*Please contact us to get the full demo report.

More Research Services

Microbial De novo Sequencing