Core Genome Analysis Overview

We offer comprehensive core genomic analysis solutions to empower your pan-genome population genomics research. By precisely identifying and analyzing the conserved genetic skeletons in the strains you have collected, we provide you with core insights into population structure, evolutionary dynamics, and stable phylogenetic relationships. Our services transform complex genomic data into actionable biological knowledge, laying a solid foundation for epidemiological tracking, species classification, and the discovery of highly conserved targets.

Our core genomic analysis services offer you the following key advantages:

• Definitive Phylogenetic Resolution: Utilize the stable signal of the core genome to construct high-resolution, reliable population phylogenies, essential for tracking transmission pathways and understanding true evolutionary histories.
• High-Efficiency SNP Discovery: Move beyond noisy accessory genomes. Our targeted analysis of core genomic SNPs provides a streamlined, high-quality variant dataset for robust population genetics and GWAS studies.
• Customized Comparative Frameworks: We tailor analysis scales to your project, from defining core genomes across closely related isolates to performing large-scale comparative studies across entire species or genera.
• Accelerated Research Timelines: Leverage our optimized pipelines and expert interpretation to swiftly distill clarity from population-scale data, significantly speeding up your analysis phase and accelerating downstream research and development.

What Is Core Genome Analysis

Core genome analysis is a methodological approach in pan-genome research, focusing on analyzing the set of genes shared by all individuals within a specific population or species. This method constructs a stable genetic framework by identifying and analyzing these shared conserved sequences. Because it filters out variable accessory genes, thereby revealing the essential genetic backbone of a species, it is of fundamental significance for determining reliable phylogenetic relationships, understanding population structure, and tracing long-term evolutionary history.

How We Deliver This Solution

Sample Collection & Preparation

To ensure the high reliability and robustness of the core genome analysis, we implement a strict and standardized workflow from sample origin. A defined genetic framework built from shared, conserved sequences requires input data of the highest consistency and quality.

• Tailored Sampling Strategy & Collection

  Based on your specific research goals (e.g., phylogenetic inference, population genetics), we design professional sampling strategies covering cohort size and diversity. Acceptable sample types include fresh or frozen tissues, whole blood, saliva, or microbial isolates, with preference for samples of high molecular integrity (avoiding long-term or improperly preserved specimens). We provide customized collection protocols to standardize this critical first step.

• Standardized Processing & Logistics

  From initial collection to sample stabilization, the entire process utilizes standardized operating procedures (SOPs) and professional reagents. Samples are aliquoted and preserved appropriately (e.g., with stabilizers or immediate freezing) to protect nucleic acid integrity. Strict cold-chain logistics and comprehensive information traceability management are implemented throughout transportation. Required sample amounts are as follows:

  • Plant tissue: ≥1 g
  • Animal tissue: ≥0.5 g
  • Mammalian whole blood: ≥1 mL
  • Whole blood with nucleated RBCs (e.g., avian, fish): ≥0.5 mL
  • Cultured cells: ≥5 × 10⁶ cells (log-phase growth recommended)
  • Purified DNA: Total mass ≥300 ng, concentration ≥10 ng/µL
• Foundational Quality Control

  Prior to analysis, all samples undergo rigorous QC checks to ensure data professionalism and authenticity, which is fundamental for defining a stable core genome.

  • DNA Quality Standards: Purity (OD260/280 between 1.8–2.0), integrity (clear electrophoretic bands without smearing indicating high molecular weight), and absence of significant RNA/protein contamination.

Sequencing

High-Quality Genome Sequencing & Assembly: For novel isolates, we employ long-read and/or high-coverage short-read sequencing to produce complete, closed genomes or high-quality draft assemblies. This is crucial for accurate pan-genome construction.

Whole-Genome Resequencing: For population studies, we utilize WGS to comprehensively capture genetic variations across all samples. Compared to targeted methods, WGS is essential for unbiased identification of core and accessory genomic regions, forming the basis for a comprehensive pan-genome.

Bioinformatics

Pan-Genome Construction & Core Genome Identification: We begin by annotating all input genomes and clustering their predicted genes into ortholog groups. This defines the species pan-genome. From this, we precisely identify the core genome—the set of genes present in all (or a defined high threshold of) studied isolates, which forms the stable backbone for downstream analysis.

Core genome alignment and SNP detection: We perform multiple sequence alignments on the identified core genomic regions. From this comparison, we extracted high-quality single nucleotide polymorphisms (SNPS) with phylogenetic information and filtered out recombination regions to ensure the clarity of the signal.

Population Genomics and Evolutionary Analysis: Based on the SNP matrix of the core genome, we conduct in-depth population genetic analysis. This includes constructing high-resolution phylogenetic trees, clarifying population structure (for example, through PCA or ADMIXTURE models), and inferling evolutionary relationships and propagation dynamics within the population.

Selection Pressure & Functional Analysis: We analyze the core genome for signatures of natural selection. By calculating metrics like dN/dS ratios across core genes, we identify genes under purifying or positive selection, linking evolutionary pressures to essential biological functions.

Service flowchart

Figure 1: How We Deliver This Solution: Core Genome Analysis Workflow

Our Advantages

Strict data fidelity: Our process begins with the quality control and standardized data management of uncompromising. This ensures that each analysis is built on highly complete genomic data, thereby minimizing human interference and maximizing the biological validity of your research results.

Improve the accuracy and resolution of phylogeny and classification: Core genes usually evolve slowly, are inherited vertically, and are less affected by horizontal gene transfer. Phylogenetic trees constructed based on single nucleotide polymorphisms (SNPS) or polygene sequences of core genes can more truly reflect the evolutionary history (vertical genetic relationship) of species, providing a more reliable basis for strain typing, traceability and population structure analysis.

Provide a standardized comparison framework: The core genome offers a unified and repeatable benchmark for comparing data from different studies and laboratories. By comparing the core genomes of different populations or ecological niches, the functional differences and evolutionary relationships can be stably evaluated.

Applications

Pathogen monitoring and traceability: Core genomic SNP typing (cgMLST/cgSNP) of outbreak strains of pathogenic bacteria (such as Salmonella, Mycobacterium tuberculosis, Vibrio cholerae) can achieve high-resolution traceability and precise tracking of the transmission chain.

Virulence and drug resistance assessment: On the basis of clarifying the background of the core genome, the acquisition and loss of accessory genomes (plasmids, virulence islands, and drug resistance gene boxes) can be analyzed more clearly, and the evolutionary dynamics of virulence and drug resistance can be understood.

Exploring speciation and adaptive evolution: By comparing the core genomes of strains from different environments or hosts, identify key genes subject to positive selection or purified selection, and reveal the genetic basis driving species differentiation and environmental adaptation.

Vaccine & Diagnostic Target Discovery: Bioinformatics screening was conducted on the core genomes of pathogens, especially difficult-to-culture bacteria, to predict surface-exposed and highly conserved proteins as potential broad-spectrum vaccine candidate antigens. For instance, this strategy has been applied in the development of vaccines against Group B streptococcus (GBS) and meningococcus.

Microbial species definition and taxonomy: Average Nucleotide Identity (ANI) of the core genome is a key genomic standard for microbial species delineation, with a widely adopted threshold of approximately 95–96% (depending on the taxonomic group and computational method). This analysis helps clarify phylogenetic relationships among closely related species or subspecies and resolves ambiguities in traditional classification systems.

Demo

Figure 2: Midpoint-root phylogenomic tree of 413 Pseudomonas genomes inferred from the concatenation of 393 core protein sequences using IQ-TREE. Bootstrap support values ≥95% are shown as dots on interior nodes. The tree was visualized using iTOL software. (Udaondo, 2024)

Case Study

Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups.

Journal: Front Cell Infect Microbiol.

Published:2017

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