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T2T Genome Assembly Service for High-Accuracy, Gap-Free Genome Sequencing
Incomplete reference genomes often leave regulatory elements, centromeres, and repeat-rich regions unresolved—limiting your ability to fully understand gene function, genome structure, and trait inheritance. CD Genomics offers a complete Telomere-to-Telomere (T2T) genome assembly service, delivering gap-free, single-contig chromosome assemblies across plants, animals, fungi, and human genomes.
Our T2T genome sequencing pipeline integrates PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C or Pore-C scaffolding, generating high-continuity, high-accuracy genome assemblies suitable for functional genomics, evolutionary biology, and precision breeding.
Whether you're mapping agronomic traits, investigating structural variation, or building a reference for complex or polyploid organisms, our team provides end-to-end project support—from experimental design through final genome delivery—with the expertise to guide confident, publication-ready research.
At a glance:
- What Is T2T Genome Assembly and Why It Matters
- Our T2T Genome Assembly Pipeline
- Why Choose CD Genomics?
- Deliverables
- Applications of T2T Genome Sequencing
- Sample Requirements
- Demo
- Frequently Asked Questions (FAQs)
- Case Study: Telomere-to-Telomere Genome Assembly of Hexaploid Bread Wheat
What Is T2T Genome Assembly and Why It Matters
T2T Genome Assembly refers to the complete, gap-free sequencing of a genome from one telomere (the protective end of a chromosome) to the other. Traditional genome assembly methods often leave gaps in regions such as centromeres, telomeres, and repeat-rich areas, limiting the understanding of important structural and regulatory elements. T2T assembly overcomes these challenges, providing a full-length, continuous genome, which is essential for precise genetic research and applications.
Key Features of T2T Genome Assembly:
Gap-Free Chromosomes: Unlike traditional assemblies, which leave unassembled regions, T2T assembly provides single-contig chromosomes, offering a seamless representation of a species' genetic material.
Full Telomere & Centromere Resolution: T2T genome sequencing solves the problem of poorly understood telomeric and centromeric regions by using advanced sequencing technologies, including PacBio HiFi, ONT ultra-long reads, and Hi-C. This breakthrough ensures that all functional genomic regions are captured and analyzed.
Accuracy and Continuity: By employing hybrid sequencing platforms, T2T assemblies achieve exceptional chromosome-scale continuity. This ensures that key structural elements, such as gene repeats, inversions, and duplications, are resolved and represented accurately.
Why T2T Genome Assembly Matters:
Unlocking Hidden Genes: Many genes that govern key traits (e.g., disease resistance, fruit size, or color) are located in previously unresolved regions. T2T genome assemblies enable the identification of these critical elements, which are often missed in fragmented genomes.
Improved Structural Variant Detection: T2T assembly provides a more accurate map of the genome, enabling better detection of structural variants (such as inversions and duplications), which are crucial for understanding genetic diversity and disease mechanisms.
Genomic Evolution & Comparative Genomics: With complete chromosome sequences, T2T assemblies offer valuable insights into the evolutionary history of species, as well as the genetic architecture that shapes their traits. They also enable cross-species comparisons to highlight conserved genetic elements.
Applications in Agriculture & Medicine: T2T genome assemblies are vital for crop improvement and drug development. In agriculture, they help to identify genes for disease resistance, drought tolerance, and yield enhancement. In medicine, T2T assemblies support the study of rare diseases and personalized medicine by providing a clearer genetic reference.
With the T2T genome assembly approach, researchers can ensure that every important genetic feature is captured and analyzed. This technology not only fills the gaps left by traditional sequencing but also unlocks new opportunities in precision genomics, functional genomics, and genetic research.
Our T2T Genome Assembly Pipeline
Sample QC & DNA Extraction
(High molecular weight DNA, RIN ≥7, >50 Kb fragments)
Sequencing Strategy:
| Strategy | Platforms | Best For |
|---|---|---|
| Hybrid T2T | PacBio HiFi (≥60×), ONT Ultra-long (≥50×), Hi-C, Illumina | High accuracy + continuity (plants, polyploids, animals) |
| ONT-only T2T | ONT Simplex reads + hifiasm(ONT) | Efficient gap-free assemblies with simplified workflow |
| HiFi-only + Hi-C | PacBio HiFi (≥60×) + Hi-C | Mid-size genomes with moderate repeats |
| Add-on: Pore-C | Optional | Enhances scaffolding & 3D genome context |
| Haplotype-resolved T2T | PacBio HiFi (≥60×), ONT Ultra-long (≥50×), Hi-C, Trio-binning | Diploid/polyploid species with high heterozygosity or complex genomes |
Assembly
- Tools: hifiasm, NextDenovo, Flye, Verkko
- Contig assembly → decontamination → gap filling → polishing
Chromosome scaffolding
- Hi-C/Omni-C or Pore-C
- Telomere and centromere extension
- Misjoin correction and manual curation
Evaluation & Quality Metrics
- BUSCO completeness
- Contig N50, telomere count
- Base accuracy (QV)
- Hi-C contact maps
- GC coverage, duplication rate
Workflow of genome assembly using HiFi reads, ultra-long reads, and HiFiasm assembly, with Hi-C validation, gap filling, and comprehensive evaluation including synteny, telomere/centromere checks, and BUSCO/CEGMA/LAI assessments.
Why Choose CD Genomics?
CD Genomics offers a one-stop service for T2T genome assembly, providing end-to-end support to ensure high-quality, gap-free genome data for your research needs.
1. Comprehensive Service Offering
- From experimental design to bioinformatics analysis to publication-ready data
- Expert guidance at every stage of your project
2. Specialized Expertise
- Over 300 genome assemblies delivered, including complex, polyploid, and repeat-rich genomes
- Proven track record in agriculture, microbial genomics, and human health
3. Advanced Technology Integration
- Using PacBio HiFi, ONT Ultra-long reads, and Hi-C, we provide gap-free, chromosome-scale genome assemblies
- Customized solutions for haplotype resolution and structural variant detection
4. Trusted by Leading Researchers
- 40+ high-impact publications backed by our high-quality genome data
- Reliable, accurate results trusted by top research institutions worldwide
Deliverables
You will receive:
- Raw sequencing data (.fastq, .bam)
- Assembly files (FASTA, GFF, annotation)
- Assembly evaluation report (BUSCO, N50, gaps, coverage)
- Visualization files (dot plots, Hi-C maps, telomere/centromere tracks)
- Optional: mutation library analysis, methylation data, or RNA integration
Applications of T2T Genome Sequencing
T2T genome sequencing is a game-changer for many areas of biological research and practical applications. By providing a complete, gap-free genome map, T2T assembly opens the door to previously hidden genetic insights.
1. Functional Genomics
- Unlock previously inaccessible genes located in repeat-rich or centromeric regions.
- Ideal for gene discovery and trait mapping in crops, animals, and microbes.
2. Evolutionary Biology
- Study chromosomal evolution and genomic rearrangements across species.
- Provides complete reference genomes for comparative genomics studies.
3. Structural Variant Analysis
- Detect structural variants such as inversions, duplications, and translocations.
- Understand genomic architecture and how structural variants impact phenotype.
4. Breeding & Agriculture
- Improve crop breeding by identifying genes for disease resistance, drought tolerance, and yield traits.
- Analyze genetic diversity in livestock, plants, and forests to accelerate breeding programs.
5. Medical & Clinical Research
- Support rare disease research with complete, accurate genomes.
- Advance precision medicine by offering a comprehensive genetic map for personalized treatment plans.
6. Microbial Genomics
- Generate high-quality reference genomes for fungi and pathogens.
- Aid in studying microbial pathogenicity, antibiotic resistance, and evolution.
Sample Requirements
| Sample Type | Recommended Input |
|---|---|
| Plant Tissue | ≥3 g |
| Animal Tissue/Cells | ≥1 g / ≥1×10⁶ cells |
| Eukaryotic Microbes | ≥300 mg wet weight or ≥1×10⁶ cells |
| Total Genomic DNA | ≥10 μg, OD260/280 ≈ 1.8, high MW (>50 Kb) |
Demo
Frequently Asked Questions (FAQs)
What is T2T genome sequencing?
T2T (Telomere-to-Telomere) genome sequencing is a comprehensive approach that aims to assemble a complete, gapless genome by sequencing from one telomere to the other, including previously unresolved regions such as centromeres and repetitive sequences. This method provides a high-quality genomic sequence characterized by exceptional accuracy, continuity, and integrity.
Why is T2T genome sequencing important?
Traditional genome assemblies often leave gaps in complex regions, limiting our understanding of genetic variation and function. T2T sequencing addresses these gaps, enabling the discovery of new genes, structural variants, and epigenetic features that are crucial for advancing research in genomics, medicine, and evolutionary biology.
What technologies are used in T2T genome sequencing?
T2T genome sequencing utilizes a combination of advanced technologies, including PacBio HiFi sequencing, Oxford Nanopore Technologies (ONT) ultra-long reads, and Hi-C scaffolding. These technologies work together to achieve high accuracy and long-read lengths, facilitating the assembly of complex genomic regions.
Which organisms can be sequenced using T2T methods?
T2T genome sequencing has been successfully applied to a variety of organisms, including humans, plants (such as Arabidopsis and maize), and fungi. The method's adaptability makes it suitable for a wide range of species, providing complete genomic information that supports diverse research applications.
How do I get started with T2T genome sequencing?
To initiate a T2T genome sequencing project, contact our team to discuss your specific research needs. We will guide you through the process, from sample preparation and sequencing to data analysis and interpretation, ensuring that you receive comprehensive and high-quality genomic data tailored to your objectives.
Case Study: Telomere-to-Telomere Genome Assembly of Hexaploid Bread Wheat
Background
The complete assembly of hexaploid wheat (Triticum aestivum) remains a major challenge in plant genomics. The hexaploid wheat genome, with approximately 15 billion base pairs and three subgenomes, is rich in repetitive sequences, making traditional sequencing methods less effective. This study presents a telomere-to-telomere (T2T) gap-free genome assembly for hexaploid wheat (cv. CS), providing critical insights into the genome's complex structure and evolution.
Methods
To achieve the gap-free assembly, the researchers employed a combination of PacBio HiFi sequencing, ONT Ultra-long reads, and Hi-C scaffolding. This hybrid approach enabled the resolution of previously unassembled regions and the assembly of complete telomeres and centromeres. The assembly process included:
- PacBio HiFi: Utilized for high-accuracy sequencing of complex genomic regions.
- ONT Ultra-long Reads: Applied for spanning repetitive sequences and telomeres.
- Hi-C: Used for chromosome-scale scaffolding and gap closure.
- Bionano: Provided additional structural data for anchoring contigs to chromosomes.
Results
The resulting CS-IAAS genome assembly, spanning 14.51 Gb, is a milestone in wheat genomics, featuring:
- Complete assembly of all 42 telomeres and 21 centromeres.
- No gaps in the chromosome sequences, making it a gap-free reference.
- Significant improvements in contig N50 (723.78 Mbp) compared to previous assemblies.
- Genome-wide insights into transposable elements, segmental duplications, and structural variations that occurred during the evolution of wheat.
Figure 1: Overview of the CS-IAAS wheat genome assembly, showing key features such as telomeres, centromeres, and structural rearrangements.
Conclusions
The T2T genome assembly of hexaploid wheat provides a comprehensive and highly accurate reference, unlocking crucial genomic features. This assembly enhances our understanding of wheat genome evolution and lays the foundation for future functional genomics studies and crop improvement. The results highlight the effectiveness of combining multiple sequencing technologies to overcome the challenges posed by complex genomes.
References
- Nguinkal JA, Zoclanclounon YAB, Brunner RM, Chen Y, Goldammer T. Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus). Sci Data. 2024 Oct 7;11(1):1095. doi: 10.1038/s41597-024-03906-9. PMID: 39375414; PMCID: PMC11458897.
- Li Q, Qiao X, Li L, Gu C, Yin H, Qi K, Xie Z, Yang S, Zhao Q, Wang Z, Yang Y, Pan J, Li H, Wang J, Wang C, Rieseberg LH, Zhang S, Tao S. Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits. Plant Commun. 2024 Oct 14;5(10):101000. doi: 10.1016/j.xplc.2024.101000. Epub 2024 Jun 10. PMID: 38859586; PMCID: PMC11574287.
- Liu, S., Li, K., Dai, X. et al. A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat. Nat Genet 57, 1008–1020 (2025). https://doi.org/10.1038/s41588-025-02137-x
- Li, H., Durbin, R. Genome assembly in the telomere-to-telomere era. Nat Rev Genet 25, 658–670 (2024). https://doi.org/10.1038/s41576-024-00718-w
For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment