Pan Genome Sequencing Service

Overview

CD Genomics provides internationally leading Pan Genome sequencing solutions, specifically designed to decode the genetic secrets of ancient organisms. By integrating targeted capture techniques with ultra-high-throughput sequencing platforms, we achieve in-depth analysis of highly degraded samples, enabling groundbreaking advancements in research on species evolution, pathogen research, ecological and environmental studies.

What is Pan Genome Sequencing Service

Pan-genome encompasses the complete set of genes found across all strains within a given species. This approach gives a more complete picture of genetic diversity than analyzing individual genomes alone. The pan-genome consists of the core genome and the variable (or accessory/dispensable) genome. The core genome comprises genes universally present in all strains of the species. These core genes are typically associated with fundamental biological functions and essential phenotypic traits, reflecting the evolutionary stability of the species. In contrast, the variable genome includes genes present only in a subset of strains or individuals. These accessory genes often encode specific adaptations or unique traits, such as antibiotic resistance genes or virulence factors. By comprehensively studying the pan genome, researchers can elucidate the full spectrum of genetic variability within a species. This facilitates a deeper understanding of its evolutionary dynamics, functional adaptations, and potential responses to environmental pressures.

Schematic image of the pan-genome structure. (Muzzi, et al., 2007)

System diagram of pan-genome construction subsystem. (Duan, et al., 2019)

Sequencing Platforms

NextSeq 500

Illumina NovaSeq

PacBio Sequel II

Workflow of Pan Genome Sequencing in Population Genetics

Our Pan Genome sequencing service workflow includes sample collection, library preparation, high-throughput sequencing, quality control, and detailed variant analysis to uncover genetic variations and population insights. Customers are encouraged to ensure proper sample handling and share specific research goals for tailored analysis. For any questions about sample requirements, sequencing, or data interpretation, our team is always ready to assist.

Bioinformatics Content

Basic Analysis	Advanced Analysis
Raw Data Quality Control: Per-base sequence quality, GC content distribution and adapter contamination ratio. Variant Calling: SNP and indel identification.Detect presence/absence variations (PAVs), copy number variations (CNVs), and inversions Gene Prediction and Annotation: Functional annotation and structural annotation. Core/Accessory Gene Analysis	Population Genetics: Phylogenetic trees, population structure analysis. GWAS and Trait Association: Use pan-genome as reference to improve precision in trait-gene mapping. Domestication and Evolution: Compare gene loss/retention between wild and cultivated species.

Why CD Genomics

Cutting-edge Sequencing Platforms: Compatible with NGS (Illumina) and third-gen (PacBio/Nanopore) platforms.
High-throughput, High-quality Sequencing: Deliver premium-quality sequencing data faster, at lower cost, and with unmatched efficiency.
One-Stop Service: End-to-end analysis from raw data QC, variant calling to population structure analysis, and provide expert data interpretation support.
Integration of Comprehensive Genomics Analysis: Offer various omics technology services, including advanced and customized genomics analysis solutions.

Sample Requirements

Sample Type: Genomic DNA.
The Required Amount of Sample DNA:

Small fragment library: ≥1 μg
2 Kb to 6 Kb large fragment library: ≥20 μg
10 Kb large fragment library: ≥30 μg
20 Kb and 40 Kb large fragment libraries: ≥60 μg;
For whole-genome sequencing: approximately 500 μg to 1 mg

Sample Purity: OD260/280 ratio should be between 1.8 and 2.0.
All DNA should be RNase-treated and should show no degradation or contamination.

Demo Results

Small variant sites in pan genome graphs.

Number of SVs present in each of the 3,202 1KG samples.

Length distribution of SV insertions and SV deletions contained.
(Liao et al., Nature, 2023）

Case Study

A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

Journal: Nature Genetics

Published: 2024

https://doi.org/10.1038/s41588-024-01715-9

Arabidopsis thaliana, a widely distributed model organism, is important for population genomics. Currently, most studies on its genome structural variations only examine a few strains. To address this, this study built a pangenome using 72 globally diverse strains (chromosome-level genome assemblies of 69 accessions) from Europe, Asia, Africa, North America, and islands. It used long-read sequencing (PacBio/Nanopore) with short-read correction (Illumina) for de novo assembly and comparative analysis. Results show The overall structure of its DNA remains very similar across different strains. And Differences in genome size are mainly caused by variations in the centromere regions. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.

Pan-genome analyses

To infer the evolutionary relationships among A. thaliana accessions, they constructed a species tree of the accessions, which confirmed their evolutionary relationships and was consistent with

previous reports highlighting the African populations as the most divergent and probably most ancient lineages.

Phylogenetic tree based on SNPs in the 72 A. thaliana genomes.

This study identified 32,986 gene families. Among these, 19,721 (60%) comprised the core genome enriched in fundamental metabolic and developmental functions. While the remaining 13,265 (40%) constituted the accessory genome, including 5,582 dispensable genes and 6,070 accession-private genes. Core genes encode significantly longer proteins containing more Pfam domains, exhibit higher expression levels, and show lower Ka/Ks ratios, indicating stronger purifying selection. Accessory genes are functionally enriched in defense responses such as disease resistance, yet notably, a substantial portion remains expressed in the reference accession Col-0.

The annotated protein-coding genes in each individual accession.

The number and proportion of core, softcore, dispensable and private gene families in the pan-genome.

The protein length, number of annotated Pfam domains, gene expression landscape and Ka/Ks of core (red), softcore (blue), dispensable (green) and private (purple) genes of Col-0.
(Lian, et al., 2024)

FAQs

How many samples are required for pan-genome analysis?

A minimum of two individuals or subspecies is required to begin a pan-genome study. However, to capture a species' full genetic diversity, more samples are recommended. Including additional samples significantly improves the resolution of genetic variation and yields a more refined pan-genome map.

Is a reference genome required for pan-genome analysis?

Pan-genome analysis does not universally require a reference genome; its dependency hinges on the assembly method. The iterative approach needs an initial reference genome for aligning all sample data, followed by independent assembly of unmapped sequences and their integration to expand the pan-genome. Conversely, the de novo assembly method operates without any reference genome, directly assembling each sample' s data into draft genomes, which are then integrated into the pan-genome via comparative genomics.

References

MUZZI A, MASIGNANI V, RAPPUOLI R (2007) The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. Drug Discov Today 12(11-12):429-439. https://doi.org/10.1016/j.drudis.2007.04.008
Duan Z, Qiao Y, Lu J et al (2019) Hupan: a pan-genome analysis pipeline for human genomes. Genome Biol 20(1):149. https://doi.org/10.1186/s13059-019-1751-y
Liao W, Asri M, Ebler J et al (2023) A draft human pangenome reference. Nature 617(7960):312-324. https://doi.org/10.1038/s41586-023-05896-x
Lian Q, Huettel B, Walkemeier B et al (2024) A pan-genome of 69 arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat Genet 56(5):982-991. https://doi.org/10.1038/s41588-024-01715-9

* Designed for biological research and industrial applications, not intended for individual clinical or medical purposes.