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Pan-Genome Sequencing

Service Overview
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pan-genomeThe pan-genome is the superset of all the genes present within a species, ranging from "core genome" genes shared by all strains to “dispensable genome” or “unique genes” present in subset of strains or only in an individual strain.

Next-generation sequencing and state-of-the-art assembly algorithms make construction of pan genome, individual, multiple strains maps feasible and provide unprecedented opportunities to investigate detailed genetic diversity at population levels. Examples of applications include breeding studies for identifying the genetic basis for desirable traits in wild and cultivated strains, and molecular ecology studies on the adaptive evolution of species across different habitats.

Novogene is a pioneer and world leader in the assembly and analysis of pan-genome maps. Our pan-genomic research studies have been published in leading scientific journals, and we provide our customers with the same high-quality data and analyses.



The Novogene Advantage

  • Highly experienced: extensive experience in pan-genome assembly and analysis with publications in top-tier journals.
  • Cost effective: less expensive than de novo sequencing, pan-genome allows the discovery of species-wide and strain-specific genes.
  • Comprehensive bioinformatics: reveals structural variations (SV), copy number variations (CNV), and presence/absence variations (PAV) that may be missed when only resequencing highly similar regions.

Project Workflow

Pan Genome analysis workflow

Sequencing Strategy

  • HiSeq platform, paired-end 150 bp

Data Quality Guarantee

Simple Genome SequencingPan-genome FrameworkContig N50 ≥ 10kb, Scaffold N50 ≥ 100kb
Pan-genome Fine MapContig N50 ≥ 20kb, Scaffold N50 ≥ 1Mb
Complex Genome SequencingPan-genome FrameworkContig N50 ≥ 10kb, Scaffold N50 ≥ 50kb
Pan-genome Fine MapContig N50 ≥ 20kb, Scaffold N50 ≥ 300kb

Sample Requirements

  • DNA amount: ≥ 400 ng

Turnaround Time

  • Depending on the project and number of samples. Please contact us to learn more.

Recommended Sequencing Depth

  • Simple genome: 80X - 100X
  • Complex genome: 100X - 200X

Analysis Pipeline

pan genome analysis pipeline

Researchers from Novogene, the Chinese Academy of Agricultural Sciences, Peking University and other institutes have used pan-genome analysis to characterize the genetic diversity of soybean and identify genetic differences potentially associated with important agronomic traits. This study published in Nature Biotechnology (Impact Factor: 39.08) facilitates the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.
Nature Biotechnology, 32:1045 (2014).

Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments.


Figure. Heatmap for CNV of resistance-related PFAM gene categories across all accessions