Pan-Genome Analysis

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Pan-Genome Analysis

With the development of genomics, such as advances in sequencing technologies and assembly methods, and lower sequencing costs, more and more new genomes have been sequenced. Researchers and professionals have realized that a single reference genome is not sufficient to achieve many research goals. To better explore genetic variation among individuals within a species, pan-genome analysis has been established and utilized.

Overview of Pan-Genome Analysis

DNA helix.

Pan-Genome refers to a collection of genetic compositions of a species, including dispensable genome (a variable set of genetic components, including unique and accessory genes) and a core, conserved genome. Among them, core genes are genes shared among all individuals of a species and are associated with the biological functions and major phenotypic characteristics of the species. The dispensable genes, also known as non-essential genes, are present in only a few samples of a species and are generally associated with species-specific adaptations to a particular environment or unique biological traits. Through high-throughput sequencing and bioinformatics analysis, individuals of different subspecies that are intrinsically related can be sequenced and individually assembled to analyze the pan-genome, which not only can obtain multiple genomic information and improve the gene set of the species, but also provide access to individual-specific DNA sequences and functional gene information, contributing to understanding the molecular evolutionary mechanism of species formation and its relationship with natural selection.

Sequencing Strategies Offering at CD Genomics

-Specie types:
Simple genome (genome size <2Gb, heterozygosity <0.5%, repeated sequence ratio <50%);
Complex genome (genome size >2Gb, heterozygosity >0.5%, repeated sequence ratio >50%);

-Sequencing data types:
ONT long reads.
ONT ultra-long reads.
PacBio continuous long reads (CLRs).
PacBio HiFi reads.

Workflow of Our Services

The study of pan-genomes begins with the sampling of a diverse set of individuals. The characterization of pan-genomes and the study of structural variations within species can reveal a wide range of variations in genome content among individuals within species.

Workflow of Our Services-CD Genomics

Analysis Pipeline and Contents

Pan-Genome Analysis
Pan-genomic profiling Analysis of genetic structural variation Additional analysis
Core and dispensable gene statistics SNP/InDel detection and annotation Identification of novel genes
 Trends in core and dispensable gene changes SV detection and annotation Phylogenetic analysis
Functional enrichment analysis CNV detection and annotation Construction of regulatory networks for core and dispensable genes

Our Service Support

  • Genetic exploration of strain traits.
  • Origin and evolution of species.
  • Adaptive evolution research.

Studies have demonstrated that pan-genomics can promote more comprehensive variant characterization, and therefore has the potential to enhance many genomic analyses. Using long-read sequencing technologies, including PacBio SMRT sequencing and Oxford Nanopore sequencing, CD Genomics is able to sequence and assemble different but interrelated individual materials at a higher depth to construct a pan-genomic map and decode the complete genetic information of the species. If you have additional requirements or questions about our services, please feel free to contact us. We’ve got everything covered for your needs and looking forward to hearing from you.


  1. Sherman, R. M., & Salzberg, S. L. (2020). Pan-genomics in the human genome era. Nature Reviews Genetics, 21(4), 243-254.
  2. Mascher, M., et al. (2021). "Long-read sequence assembly: a technical evaluation in barley." The Plant Cell, 33(6), 1888-1906.
  3. Della Coletta, R., et al. (2021). "How the pan-genome is changing crop genomics and improvement." Genome biology, 22(1), 1-19.
For Research Use Only. Not for use in diagnostic procedures.

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