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Animal and Plant De novo Sequencing

Introduction to Animal and Plant De novo Sequencing

De novo sequencing generates an initial genomic sequence of a particular organism without a reference sequence. Through de novo sequencing, complex genomic variations such as Indel, CNV, and SV can be easily identified. It is also valuable in evolutionary and demographic history, agricultural breeding, and genetic variations calling.

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 you ultra-fast turnaround time.

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 Revio/Sequel II/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%.

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 Sequel IIe DNA CLR library HMW Genomic DNA ≥ 5 μg A260/280=1.75-2.0;
A260/230=1.5-2.6;
*NC/QC=0.95-3.0;

Fragments should be ≥ 30 kb
PacBio Revio/Sequel IIe DNA HiFi library HMW Genomic DNA ≥5 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 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 Parameters Illumina Novaseq 6000 PacBio Revio/sequel II/sequel IIe Nanopore PromethION
Read Length Paired-end 150 bp N50>15 kb, long read lengths up to 25 kb（CCS） average > 17 kb
Recommended  Sequencing Depth For genome survey or assembly polishing: ≥ 50× For genome assembly: ≥ 50×
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

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.

 

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