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Research Services

Animal and Plant De novo Sequencing

Introduction to Animal and Plant De novo Sequencing

De novo sequencing involves sequencing and assembling the genome of a species without relying on a reference genome, using ‌PacBio long-read sequencing and Oxford Nanopore‌ long-read sequencing‌ to construct 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.

To achieve the highest accuracy in genome assembly, Novogene leverages ‌PacBio Revio and ‌Oxford Nanopore‌ PromethION platforms, delivering unparalleled contiguity for complex genomes. Our integrated approach combines Hi-C sequencing for chromosome-scale scaffolding, mRNA sequencing and full-length isoform sequencing for genome annotation. This multi-platform strategy enables us to deliver ‌well-annotated, chromosome-level genomes‌.

Applications of Animal and Plant De novo Sequencing

For individual research：

  • Guides animal health and genetic breeding
  • Provides a theoretical basis for drug screening
  • Explores medicinal resources and innovates varieties

For population research：

  • Explores species origin and evolution
  • Provides new insights into patterns of genome divergence

Benefits of Animal and Plant De novo Sequencing

  • Highly experienced: Novogene’s highly qualified researchers have completed major De novo genome sequencing projects and managed to publish their data in top-tier journals.
  • Bioinformatics expertise: Best-in-class and widely recognized software, such as Falcon and Canu, are being used for comprehensive plant and animal bioinformatic analyses.
  • Diverse strategies: By incorporating sequencing results from various platforms including Illumina Novaseq, PacBio PacBio Revio/Sequel IIe, and Oxford PromethION, we offer the best assembly solution specifically tailored for each unique genome.
  • Unsurpassed data quality: We guarantee a Q30 score ≥ 85%, exceeding Illumina’s official guarantee of ≥ 75%.

On Demand Webinar

A Beginner’s Guide to Animal and Plant Whole Genome Sequencing – Re-Sequencing and De novo sequencing with Novogene

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Animal and Plant De novo Seq Specifications:
DNA Sample Requirements

Platform Type Sample Type Amount (Qubit®) Purity

Illumina

NovaSeq X Plus /

NovaSeq 6000

Genomic DNA

≥ 200 ng

OD260/280=1.8-2.0;

no degradation, 
no contamination

Genomic DNA

(PCR free non-350bp)

≥ 3 μg

Genomic DNA

(PCR free 350bp)

≥ 1.1 μg
PacBio Revio DNA HiFi library HMW Genomic DNA ≥ 3 μg A260/280=1.75-2.0;
A260/230=1.5-2.6;
*NC/QC=1.0-2.2

Fragments should be ≥ 30 kb
PacBio PCR product
library		 PCR product ≥ 2 μg OD260/280=1.75~2.0;
OD260/230=1.4~2.6;
*NC/QC=0.95~3.00; Single band
(PacBio library fragments
distributed above 1k)
Nanopore
PromethION DNA library		 HMW Genomic DNA ≥ 8 μg A260/280=1.75-2.0;
A260/230=1.4-2.6;
*NC/QC=0.95~3.00

Fragments 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.
Nanopore PCR
product library		 PCR product ≥ 2 μg OD260/280=1.75~2.0;
OD260/230=1.4~2.6;
*NC/QC=0.95~3.00; Single band

NC/QC:NanoDrop concetration/Qubit concentration

Animal and Plant De novo Seq Specifications:
Sequencing and Analysis

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 Ultra-long reads N50 > 50 kb or 100 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
Advanced Analysis –

Comparative genomics

Pan-genome analysis

Telomere-to-telomere genome assembly

Perfect telomere-to-telomere genome assembly

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.





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.

 

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