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 6000 |
Genomic DNA | ≥ 200 ng | A260/280=1.8-2.0; no degradation, no contamination |
Genomic DNA (PCR free non-350bp) |
≥ 5 μg | ||
Genomic DNA (PCR free -350bp) |
≥ 1.2 μg | ||
PacBio Sequel II DNA CLR library |
HMW Genomic DNA | ≥ 5 μg (Concentration ≥ 70 ng/μL) |
A260/280=1.75-2.0; A260/230=1.5-2.6; NC/QC=0.95-3.00 Fragments should be ≥ 30 kb |
PacBio Revio/sequel II/sequel IIe DNA HiFi library | HMW Genomic DNA | ≥ 9 μg (Concentration ≥ 70 ng/μL) |
A260/280=1.8-2.0; A260/230=1.5-2.6; NC/QC=1.00-2.20 Fragments should be ≥ 30 kb |
Nanopore PromethION | HMW Genomic DNA | ≥ 8 μg (Concentration ≥ 100 ng/μL) |
A260/280=1.75-2.0; A260/230=1.4-2.6; NC/QC=0.95-3.00 Fragments should be ≥ 30 kb |
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 | ||
Recommended Sequencing Depth | For genome survey or assembly polishing: ≥ 50× | For genome assembly: ≥ 50× | |
Standard Analysis
|
|
|
|
Genome Annotation | - |
|
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
-
Science Advances Date: April 2020IF: 12.804DOI: https://www.science.org/doi/10.1126/sciadv.aay3240
-
Deciphering the High Quality Genome Sequence of Coriander that Causes Controversial Feeling
Plant Biotechnology JournalIssue Date:2019IF: 6.84DOI: https://onlinelibrary.wiley.com/doi/10.1111/pbi.13310
-
Chromosome-level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)
Molecular Ecology ResourcesIssue Date: July 2019IF: 7.049DOI: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13086
-
Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Plant Biotechnology JournalIssue Date: 2019IF: 6.84DOI: https://onlinelibrary.wiley.com/doi/10.1111/pbi.13205
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
