TL;DR – How eccDNA connects humans, plants, and animal models

Extrachromosomal circular DNA (eccDNA) is a circular DNA molecule that originates from chromosomal DNA but exists outside chromosomes in the nucleus. It has been reported in humans, plants, and a wide range of model organisms, where it relates to genome plasticity, stress responses, gene amplification, and disease.

This article compares eccDNA humans, eccDNA plants, and eccDNA animals, then translates those insights into practical design tips for multi-species eccDNA sequencing projects, including Circle-seq and follow-up eccDNA qPCR quantification.

Why is eccDNA across humans, plants, and animals now a cross-species research priority

eccDNA across species is now viewed as a shared genomic feature rather than a rare artifact. Reports from different fields—cancer biology, plant stress biology, yeast genetics, and developmental systems—converge on the same message: circular DNA derived from the nuclear genome appears in many eukaryotic organisms and in both healthy and diseased states.

For researchers, this raises three practical questions:

• Is eccDNA just a byproduct, or can it shape phenotype and evolution?
• Can we compare eccDNA profiles across humans, crops, and model organisms in one study?
• How do we design eccDNA sequencing and bioinformatics to handle multiple genomes at once?

From a project perspective, cross-species eccDNA analysis can:

• Reveal common mechanisms of DNA damage and repair.
• Highlight genome plasticity in stress, drug resistance, or adaptation.
• Suggest new biomarkers that are conserved rather than species-specific.

This is where a structured eccDNA Sequencing (Circle-seq) workflow and robust bioinformatics become essential. A unified experimental backbone lets you ask the same biological question in humans, plants, and animal models and compare eccDNA patterns in a consistent way.

Cross-species timeline of eccDNA discoveries. Overview of key milestones in eccDNA research from early observations in boar sperm and wheat to more recent findings in yeast, ciliates, amphibians, birds, rodents, and humans, highlighting how eccDNA has emerged as a ubiquitous feature of eukaryotic genomes (Zuo S. et al. (2022) Frontiers in Cell and Developmental Biology).

What is eccDNA and how conserved is it from humans to plants and model organisms

eccDNA is circular DNA derived from chromosomal sequences that reside outside chromosomes in the eukaryotic nucleus.

Unlike mitochondrial DNA or bacterial plasmids, eccDNA:

• Originates from the nuclear genome rather than an organelle or pathogen.
• It can span a wide size range, from a few hundred bases to megabase-scale circles.
• Often contains exons, regulatory elements, repeats, or even full genes.

Across species, several themes emerge:

• Formation mechanisms show shared principles.

  Many eccDNA formation models involve DNA repair pathways such as non-homologous end joining, alternative end joining, and homologous recombination. These mechanisms have been studied in both human cancer models and classic organisms like yeast.

• Functional roles are multi-layered.

  eccDNA can contribute to gene amplification, epigenetic remodeling, telomere dynamics, and gene regulation, with potential roles in aging, development, and disease.

• Ubiquity suggests evolutionary importance.

  eccDNA has been described in organisms as diverse as wheat, boar sperm, yeast, ciliates, amphibians, birds, rodents, and humans. The recurrence of this phenomenon across phylogeny has led to growing interest in eccDNA evolutionary studies.

Together, these observations support the idea that eccDNA is a general feature of eukaryotic genomes and not confined to a single lineage or disease state.

Mechanisms and downstream functions of eccDNA. Schematic overview of how DNA damage, replication stress, and recombination pathways generate eccDNA, and how these circles can influence transcription, telomere maintenance, genome stability, immune signaling, and cell–cell communication in different organisms (Zuo S. et al. (2022) Frontiers in Cell and Developmental Biology).

eccDNA in humans: genomic hotspots, functional clues, and disease links

Human eccDNA refers to nuclear circular DNA molecules derived from the human genome, detected in normal and disease tissues.

Key features in human samples

Studies on eccDNA humans – that is, eccDNA in human samples – report several recurring characteristics:

• A broad size spectrum, including small "microDNA" (often a few hundred base pairs) and larger circles, including oncogene-bearing ecDNA in tumors.
• Enrichment in gene-dense regions, exons, and CpG islands, suggesting a connection to active chromatin and transcription.
• Presence in plasma, tumor tissue, and normal tissues, with distinct eccDNA profiles between conditions and tissue types.

Functionally, human eccDNA has been implicated in:

• Cancer biology.

  Large eccDNA species (often referred to as ecDNA) can carry oncogenes and regulatory elements, contributing to high-level gene amplification, transcriptional rewiring, and tumor heterogeneity.

• Immune and stress responses.

  Some eccDNA species may act as danger signals or influence gene expression during inflammation, replication stress, or DNA damage responses.

Practical tips for the human eccDNA projects

When designing an eccDNA Sequencing (Circle-seq) project in human samples, a few practical points help:

• Use high-quality, minimally sheared DNA from fresh or well-preserved biopsies or blood-derived DNA to avoid losing longer circles.
• Include matched controls, such as adjacent non-tumor tissue or baseline plasma, to distinguish disease-associated eccDNA from background levels.
• Plan sufficient read depth to capture low-abundance eccDNA species, especially if you are interested in oncogene-bearing circles or rare immune-related eccDNA species.

Because human projects often relate to translational or biomarker questions, they benefit from integrated eccDNA Research Solutions—covering study design, sequencing, and downstream interpretation—rather than isolated steps.

eccDNA in plants: stress responses, genome plasticity, and agronomic traits

Plant eccDNA comprises circular DNA molecules derived from plant nuclear genomes, often carrying repeats, stress-related elements, or coding sequences.

Plant genomes are typically rich in repetitive sequences and transposable elements, and plant eccDNA reflects this structure. Reports on eccDNA plants describe:

• Abundant circles containing repetitive or intergenic sequences.
• Occasional large eccDNA molecules carrying full genes and adjacent regulatory regions.
• eccDNA profiles that change under environmental or chemical stress.

One widely discussed case involves eccDNA carrying the EPSPS gene in a weed species, where gene amplification on large circular DNA contributes to herbicide resistance. This highlights eccDNA as a mechanism for rapid adaptation in an agricultural context.

Why eccDNA matters for plant biologists

For plant biology and breeding, eccDNA can:

• Reflect the environmental stress history, with circles enriched for stress-responsive genes or repeats.
• Reveal genome plasticity in crops and wild relatives, complementing conventional structural variant analysis.
• Provide targets for monitoring resistance evolution, such as eccDNA associated with herbicide tolerance or other agronomic traits.

Practical tips for eccDNA plants sequencing

When planning an eccDNA sequencing project in plants:

• Optimize tissue handling for each species. Leaves, roots, seeds, and callus may require distinct lysis and purification strategies because of cell walls and secondary metabolites.
• Include treatment-based comparisons (e.g., unstressed vs stressed, susceptible vs resistant lines) to clearly link eccDNA patterns to phenotype.
• Consider reference genome quality. Non-model crops or landraces may have fragmented assemblies; analysis pipelines should tolerate variable reference quality and handle repeats carefully.

Plant projects are a natural fit for custom eccDNA Research Solutions, where protocol and analysis tailoring can unlock insights from complex or polyploid genomes.

eccDNA in model organisms and cell systems: from yeast to mice

Model-organism eccDNA includes circles in yeast, invertebrates, and vertebrate systems that facilitate mechanistic and time-course studies.

Yeast and aging

In budding yeast, extrachromosomal rDNA circles are a classic example of eccDNA. These circles accumulate in aging cells and have been proposed as one factor in replicative aging. Yeast therefore provides an experimentally tractable system for dissecting eccDNA biogenesis, segregation, and impact on cellular lifespan.

Quantitative eccDNA mapping in ageing yeast. (Hull R.M. et al. (2019) PLOS Biology).

Invertebrate and vertebrate models

In animals, eccDNA animals have been detected in:

• Invertebrates such as Drosophila and nematodes, where eccDNA can contain transposon-derived sequences and other genomic elements.
• Vertebrate models such as Xenopus and mice, often in developmental or disease contexts.

Mouse embryonic stem cells and engineered tumor models are especially useful for:

• Introducing defined DNA lesions or oncogenes and monitoring eccDNA formation.
• Performing time-course experiments to track eccDNA accumulation and clearance.
• Testing how genetic background or pathway perturbations influence eccDNA profiles.

Practical design notes for model systems

When integrating eccDNA into model-organism projects:

• Align sampling time points with key biological events, such as differentiation milestones, treatment windows, or disease progression stages.
• Use biological replicates for each condition to ensure robust statistical comparison.
• Plan shared controls across related experiments where possible, especially for large Circle-seq runs that include multiple conditions or cell lines.

Because model systems can generate many samples, pairing discovery-scale Circle-seq with scalable eccDNA qPCR quantification is often cost-effective. Sequencing identifies candidate eccDNA species; targeted qPCR then tracks these circles across broader cohorts or dose-response series.

Cross-species patterns: what eccDNA teaches us about genome evolution and adaptation

Cross-species eccDNA studies compare circles across organisms to understand how genomes respond to stress and selection.

When we place eccDNA humans, eccDNA plants, and eccDNA animals side by side, several patterns emerge that are useful for both basic and applied research.

Cross-species comparison at a glance

Below is a simplified comparison of eccDNA features across major organism groups:

The exact distributions depend on species, tissue, and experimental protocol, but some consistent themes emerge.

Interpreting these patterns

From an evolutionary perspective, eccDNA appears to:

• Offer rapid, reversible changes in gene copy number, especially under strong selection such as herbicide exposure or drug treatment.
• Reflect local genome structure, including repeats and fragile sites that are prone to recombination or repair.
• Serve as a record of genome stress, particularly when eccDNA is associated with DNA damage, replication stress, or chromatin remodeling.

These observations motivate eccDNA evolutionary projects that explicitly compare circles across species to understand how genomes flex and adapt under pressure.

Designing eccDNA sequencing projects that span humans, plants, and non-model species

A cross-species eccDNA sequencing project uses a unified experimental and bioinformatics strategy to profile eccDNA in multiple organisms.

Experimental and computational approaches for eccDNA research. (Zuo S. et al. (2022) Frontiers in Cell and Developmental Biology).

This section translates biological insight into concrete design guidelines.

Choosing sample types and inputs

For multi-species eccDNA Sequencing (Circle-seq) projects, typical sample types include:

• Human: Tumor biopsies, resected tissue, whole blood, plasma, or cultured primary cells and lines.
• Plants: Leaves, roots, seeds, callus cultures, or stress-treated tissues.
• Animals and models: Specific organs, xenografts, engineered tumors, embryos, or in vitro cell systems.

Practical suggestions:

• Standardize collection and storage wherever possible, for example by snap-freezing tissue in liquid nitrogen or using validated nucleic acid preservation tubes for blood.
• Aim for consistent DNA input ranges across samples while recognizing that yield per gram of tissue will differ between plants, animals, and human material.
• Capture rich metadata: genotype, developmental stage, tissue type, treatment, time point, and environmental conditions.

Controls and experimental design

Good eccDNA experimental design is comparison-driven. Consider:

• Baseline controls, such as untreated plants, untreated animals, or clinically "normal" human tissue where appropriate.
• Condition controls, such as sensitive vs resistant lines, or pre- vs post-treatment samples.
• Technical controls, including spike-in circular DNA or plasmid standards to monitor recovery, enrichment, and library performance across batches.
• Biological replicates, commonly at least three per condition, to support statistical modeling rather than relying on single representative samples.

Read depth and bioinformatics across species

Cross-species eccDNA studies require bioinformatics pipelines that can:

• Detect circular junctions reliably in each genome.
• Handle variable reference quality, from highly curated human assemblies to more fragmented plant or non-model animal genomes.
• Annotate circles with species-specific gene models, repeat annotations, and regulatory features.

Some general planning guidelines:

• For high-complexity, low-abundance eccDNA signals (such as plasma or small tumors), plan higher read depth to avoid undersampling rare circles.
• For strongly induced eccDNA (for example, in plants under intense stress or in cell lines under high-dose selection), moderate depth can still capture the key events.
• Keep species balance in mind if pooling humans, plants, and animals in the same sequencing run. One species with very complex libraries should not dominate the run at the expense of others.

After discovery, targeted eccDNA qPCR quantification is a practical way to validate and track a small set of biologically interesting circles in larger cohorts, time-course experiments, or breeding programs.

From comparative insight to action: building multi-species eccDNA studies with specialised platforms

A specialised eccDNA platform combines wet-lab, sequencing, and bioinformatics expertise to support cross-species eccDNA research from design to interpretation.

For many labs, the main bottleneck is not the scientific question but the operational complexity:

• Different extraction and lysis protocols for humans, plants, and animals.
• Diverse reference genome quality and annotation depth.
• The need to keep Circle-seq chemistry and computational analysis consistent across all species so that results are comparable.

A dedicated eccDNA Research Solutions provider can help by:

• Advising on sample collection SOPs tailored to each species, from plant tissue grinding to plasma handling and cell-culture harvesting.
• Designing Circle-seq or related eccDNA sequencing workflows that support mixed-species batches while controlling for technical variation.
• Implementing cross-species bioinformatics workflows, including handling of non-model genomes and custom annotations.
• Providing integrated reporting, with species-specific data summaries plus harmonized cross-species comparisons.

A typical project path for multi-species eccDNA work might look like:

1. Scoping discussion – Define species, sample types, biological questions, and success criteria.
2. Pilot eccDNA Sequencing (Circle-seq) – Run a limited set of representative samples to fine-tune protocols, depth, and analysis parameters.
3. Scale-up phase – Apply optimized workflows to full cohorts across humans, plants, and animal models.
4. Targeted follow-up – Use eccDNA qPCR quantification and other targeted assays to validate candidate eccDNA species and track them in larger or longitudinal studies.

If you are considering a multi-species eccDNA evolutionary or stress-adaptation project, this is an ideal moment to reach out, share your draft design, and explore a tailored project plan.

FAQs on eccDNA across humans, plants, and animal models

1. Is eccDNA really present in many eukaryotes, or mainly in cancer?

eccDNA has been reported in a wide range of organisms, including yeast, plants, invertebrates, and vertebrates, as well as in human tissues. Cancer is a high-visibility example because large eccDNA can carry oncogenes, but eccDNA also appears in normal cells and in non-disease contexts such as development and stress responses.

2. How does eccDNA differ between humans, plants, and model organisms?

In eccDNA humans, researchers often observe microDNA enriched in gene-dense regions, along with larger oncogene-bearing circles in tumors. In eccDNA plants, many circles are repeat-rich, and some large eccDNA molecules carry genes linked to stress adaptation or resistance traits. Model organisms, such as yeast or mice, provide systems where eccDNA can be tied to aging, development, or engineered pathways, with controlled genetic and environmental backgrounds.

3. Which method should I use to detect eccDNA across species?

Circle-enrichment sequencing approaches—often grouped under Circle-seq and related methods—are widely used for eccDNA discovery. These workflows typically combine selective enrichment of circular DNA with next-generation sequencing and dedicated analysis pipelines. For follow-up, targeted eccDNA qPCR assays are useful to validate specific circles or monitor them in larger cohorts with lower per-sample cost.

4. Can I run human, plant, and animal eccDNA samples in the same sequencing batch?

Yes, it is possible to batch multiple species in the same run, but careful design is important. You should ensure compatible library preparation chemistry and indexing, maintain reasonable balance in input and expected library complexity, and have a bioinformatics plan that cleanly separates reads by species. Working with an integrated eccDNA Sequencing (Circle-seq) service helps manage these considerations and reduce technical bias.

5. How do I link eccDNA findings to function or phenotype?

Linking eccDNA to function means annotating which genes or elements each circle carries, interpreting these circles in the context of your conditions (stress, treatment, disease stage), and then testing candidates with expression profiling, phenotypic readouts, and targeted assays such as eccDNA qPCR. Comparative designs—for example humans plus model organisms, or crops plus weeds—help highlight conserved eccDNA responses that are more likely to be biologically meaningful.

Ready to design your cross-species eccDNA study?

eccDNA is no longer a niche curiosity. From eccDNA humans in cancer and immunity to eccDNA plants in stress adaptation and eccDNA animals in development and aging, circular DNA offers a shared lens on genome plasticity across life. CD Genomics can support your cross-species eccDNA projects with research-use-only sequencing and analysis solutions.

If you are planning a cross-species eccDNA project—whether focused on evolution, stress responses, or translational biomarker discovery—consider partnering with a platform that offers:

• Dedicated eccDNA Sequencing (Circle-seq) workflows for diverse species.
• Integrated eccDNA Research Solutions spanning study design, laboratory execution, and bioinformatics.
• Follow-up eccDNA qPCR quantification to validate and scale your key findings.

You can now move from comparative eccDNA ideas to an actionable project plan by outlining your research goals, sample types, and experimental constraints and requesting a tailored eccDNA study proposal.

Related reading

• Exploring EccDNA through Circle-seq
• Comparative Analysis of eccDNA Detection Methods
• eccDNA 101: Biogenesis, Classes, and Why It Matters for Human Disease
• Designing an eccDNA Sequencing Study: Sample Types, Controls, and Read Depth