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Third-generation Animal and Plant De Novo Sequencing
Brief

De Novo sequencing refers to the technique of ab initio sequencing, splicing and assembly of the genome of a species without relying on the reference genome to obtain the single-base precision sequence map of the whole genome. After completing the whole genome sequence map, a genome library of this species can be constructed, so as to build an efficient platform for post-genomic research of this species, and provide DNA sequence information for subsequent gene mining and functional verification.

Fields
  • Genome de novo
  • Assembly promotion
  • Comparison of genetically close species
Process
6、TGS - third-generation animal and plant de novo sequencing.png
Parameters
Product TypeSequencing StrategyRecommended Data AmountCycle
Plant and animal genomes de novoHiSeq/NovaSeq/PacBio

Simple genome: survey (100X PE150), sketch (HiFi: 20-35X), Hi-C assisted assembly (100X), annotations (recommended Isoseq 50G subreads;

Complex genomes: survey (100X PE150), sketches (HiFi ≥ 30X), Hi-C assisted assembly (100X), annotations (recommended Isoseq 50G subreads).

The fastest time for genome sketch assembly is 8 natural days, and the fastest time for assembly+annotation+evolution is 50 natural days. The specific cycle depends on the complexity of the genome.
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Requirements
Product TypeSampling Requirements
Genome Survey (illumina platform)Sample type: genomic DNA sample;
Sample demand: tiny fragment library ≥0.2μg;
Sample concentration: ≥5ng/μl;
Sample purity: OD260/280= 1.8-2.2; OD260/230=0.8-2.5;
Sample quality: complete genome, clear DNA main band, free of degradation and pollution.
Genome De Novo ( PacBio platform)Total DNA: HiFi≥6.5 μg;
Concentration: 80 ng/L;
Quality: genome integrity, DNA main band: ≥30kb;
Purity: OD260/280=1.8-2.0; OD260/230=1.6-2.5; NC/QC=0.5-3.0
Genome AnnotationAt least 6 samples from different periods or parts, recommended Iso-seq ≥ 50G data volume.
Hi-C Assisted Assembly ( Illumina platform )For formaldehyde cross-linking of new blood tissues, one Hi-C library requires at least about 5 ml of fresh blood or 1 g of tissue, recommended 2-3g tissue volume.
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