T2T Genome Sequencing Service: Achieve Complete, Gap-Free Genome Sequences
Service Highlights
Compared to other genome sequencing methods, our T2T Genome Assembly service offers the advantage of delivering complete, gap-free genome sequences, including complex regions like telomeres and centromeres, which are typically challenging to sequence. By leveraging PacBio HiFi and ONT Ultra-long sequencing technologies, combined with Hi-C scaffolding, our service ensures high-resolution, chromosome-level assemblies with unparalleled accuracy, making it an efficient and reliable choice for deep genomic research across various species.
Request a QuoteService Introduction
T2T Genome Assembly (Telomere-to-Telomere Genome Assembly) is used to generate complete genome sequences, including complex regions such as telomeres and centromeres, which traditional genome assembly methods often fail to resolve. By leveraging PacBio HiFi and ONT Ultra-long long-read sequencing technologies, combined with Hi-C scaffolding, T2T assembly ensures the gap-free integrity of the genome from telomere to telomere, providing high-resolution, chromosome-level genome assemblies. This technique significantly enhances the accuracy of genomic research, offering critical data for functional genomics, genetic variation studies, and species evolution analysis.
Why Choose T2T Genome Assembly: Key Advantages
Technical Advantages
1. Complete, Gap-Free Genome
T2T genome assembly delivers a truly continuous sequence that spans every region of the chromosome—including notoriously hard-to-map areas such as telomeres and centromeres—offering researchers a fully resolved genetic blueprint.
2. Chromosome-Level Resolution
By integrating PacBio HiFi and Oxford Nanopore ultra-long read platforms, we generate assemblies at the chromosome scale. This high-resolution view provides a precise framework for studying structural organization, gene function, and genetic diversity.
3. Higher Assembly Accuracy
The use of long-read data makes it possible to resolve repetitive and complex regions that often cause errors or gaps in conventional sequencing approaches. The outcome is a highly reliable sequence with improved accuracy across challenging genomic landscapes.
4. Deeper Functional Genomic Insight
Access to an uninterrupted genome sequence allows researchers to investigate regulatory elements, gene activity, and epigenetic features with greater clarity. This comprehensive view supports advanced functional genomics studies.
5. Broad Research Utility
From mapping structural variants and characterizing evolutionary relationships to supporting plant, animal, and human studies, T2T genome assemblies provide robust datasets that accelerate discoveries across multiple scientific disciplines.
Our Service Advantages
1. Customized Study Design
No two projects are the same. We develop tailored sequencing and assembly strategies to align precisely with your research objectives, whether in agriculture, evolutionary biology, or human genetics.
2. Consistent, Dependable Outcomes
We prioritize both speed and quality. Our optimized workflows ensure that you receive results on schedule, with the accuracy and reliability needed to drive confident decision-making.
3. Dedicated Expert Guidance
Our specialists provide hands-on support from the planning stage through to data delivery. We work closely with you to ensure your T2T assembly meets your expectations and provides meaningful insights.
Service Workflow: From Sample to Genome Assembly
Our Telomere-to-Telomere (T2T) Genome Assembly workflow is carefully structured to generate highly accurate, gap-free genomes with chromosome-level continuity. The process includes the following stages:
1. Sample Collection & Preparation
High-integrity genomic DNA is essential. We provide detailed instructions to help ensure that samples are collected, handled, and preserved under optimal conditions.
2. Long-Read Sequencing
PacBio HiFi and Oxford Nanopore ultra-long sequencing platforms are applied to capture extensive read lengths, enabling complete coverage of even complex regions such as telomeres and centromeres.
3. Genome Assembly
Using advanced assembly algorithms and Hi-C data for scaffolding, we reconstruct the genome with chromosome-scale precision and structural accuracy.
4. Gap Closure & Polishing
Remaining gaps are resolved, and additional sequencing data are used to refine the assembly, ensuring maximum completeness and minimizing potential errors.
5. Bioinformatics Interpretation
Comprehensive analyses identify genetic variants, structural features, and epigenetic patterns, offering deep insights into genome organization and functional elements.
6. Final Data Package
You will receive a fully assembled genome in FASTA format, along with annotation files, variant calls, and a detailed analytical report designed to support downstream research.
By following this stepwise workflow, we provide researchers with complete, high-quality genomic data tailored to their scientific objectives.
Customer to Provide: Sample Preparation Requirements
For optimal results with our T2T Genome Assembly service, it is crucial that your samples meet the following specifications. High-quality samples ensure accurate sequencing and high-resolution genome assembly.
Genomic DNA (for De Novo Assembly)
- Amount: At least 6 μg of high-quality genomic DNA is required for HiFi sequencing.
- Concentration: ≥30 ng/μl for sequencing consistency.
- Purity:
- OD260/280: ≥1.8 (indicating pure DNA).
- OD260/230: ≥1.8 (to ensure the absence of contaminants).
- Integrity: The DNA should be high molecular weight, with clear, intact bands of ≥30 kb for HiFi sequencing. Ensure that there is no degradation or contamination in the sample.
Plant Samples
- Type: Fresh tissue (e.g., leaves, roots), or tissue culture material.
- Storage: Samples should be either silica-dried or frozen immediately to preserve DNA integrity during transport. Avoid exposure to high temperatures or humidity during transportation.
Animal Samples
- Type: Whole blood or fresh tissue (e.g., muscle, liver, or other organs).
- Storage: Preserve samples in ethanol or transport on ice to maintain DNA integrity. Ensure that samples are not degraded by improper storage or temperature fluctuations.
Hi-C Samples (for Hi-C Scaffolding)
- Type: Fresh tissue (e.g., 5 ml of blood or 1 g of tissue).
- Storage: Store and transport samples under cold conditions to preserve chromatin for Hi-C library construction.
Deliverables: What You Will Receive
Upon completion of your T2T Genome Assembly project, you will receive the following deliverables:
- Chromosome-level gap-free genome assemblies
A complete, gap-free genome with chromosome-level assembly, including contigs, scaffolds, and detailed assembly statistics to assess quality.
- Genome annotation files
Comprehensive annotation files in GFF3 format, including coding genes, non-coding RNAs, repeats, and pseudogenes, providing functional insights into the assembled genome.
- Variant and expression analysis
Profiles of genetic variants such as SNPs, INDELs, and structural variants, delivered in VCF format. Additionally, optional expression analysis for gene activity and allele-specific expression where applicable.
- Epigenetic analysis
Insights into DNA methylation and histone modification patterns (if applicable), helping to explore epigenetic regulation across the genome.
- Comparative and evolutionary insights
Optional outputs, including phylogenetic analysis, genomic comparisons, and evolutionary insights based on T2T assembly to understand species relationships and conserved genetic elements.
- Visualization and reports
Publication-ready figures such as heatmaps, Circos plots, phylogenetic trees, and a detailed analysis report summarizing key findings, assembly quality, and insights into genetic variation and gene function.
- Raw and processed data files
Complete raw data files (e.g., fastq, bam, vcf) and processed data with quality control results, providing full transparency and enabling further analysis as needed.
Service Description
| T2T Genome Type | Sequencing Platform | Recommended Depth | Assembly Metrics | Library Size |
|---|---|---|---|---|
| Gap-Free T2T | PacBio HiFi | ≥60X | At least one chromosome assembled to T2T | 15-20 kb |
| ONT Ultra-long | ≥30X | Chromosome-level assembly | 50 kb/100 kb/150 kb | |
| Hi-C | 100X | Gap-free genome | ||
| Golden T2T | PacBio HiFi | ≥60X | Full genome assembly to T2T | 15-20 kb |
| ONT Ultra-long | ≥100X | Chromosome-level, gap-free genome | 50 kb/100 kb/150 kb | |
| Hi-C | 100X | Chromosome-level assembly |
Applications of T2T Genome Assembly
T2T genome assembly offers numerous applications across a wide range of research areas, providing essential insights into complex regions of the genome that were previously difficult to study. Here are some key applications:
- Filling Genome Gaps: T2T assembly provides complete, gap-free genome sequences, ensuring no part of the genome, including telomeres and centromeres, is left unresolved. This is crucial for obtaining a fully accurate and comprehensive genome.
- Discovery of New Genes and Functions: By generating a complete genome, T2T enables the identification of novel genes, functional elements, and previously uncharacterized genetic variations, which are essential for advancing our understanding of gene function and biological processes.
- Centromere and Telomere Analysis: T2T assembly is particularly valuable for studying the highly complex centromere and telomere regions. These regions play critical roles in chromosome stability and cellular aging, and T2T helps explore their structure and functional characteristics in depth.
- Complex Structural Variation and Repeat Analysis: The ability to assemble repetitive DNA regions and structural variations with T2T technology enables a detailed examination of segmental duplications (SDs) and other genomic rearrangements that contribute to genetic diversity and disease.
- Epigenetic Mapping and Base Modification: Leveraging the power of ONT sequencing, T2T assembly allows for detailed exploration of epigenetic modifications such as DNA methylation at critical regions like centromeres, providing insights into gene regulation and chromatin structure.
- Near-Centromere Gene Exploration: T2T assembly enables the study of genes located near the centromere, offering insights into the transcriptional activity of these often-overlooked regions, which play crucial roles in cell division and genomic stability.
- Species Genetic Variation: By assembling the full genome, T2T helps identify genetic variation across species, contributing to genetic diversity studies, species evolution, and providing valuable data for conservation biology.
Case Studies
(Yang, T., Cai, Y., Huang, T., Y., et al., Horticulture Research, 2024.03).
Research Subject: West Indian avocado varietyResearch Methods: NGS, PacBio HiFi, ONT, Pore-C, FISH, RNA-seq, population re-sequencing
Research Focus:1. Using PacBio HiFi, ONT Ultra-long, and Pore-C sequencing technologies, the genome was assembled and gaps were filled, ultimately achieving a T2T-level avocado genome.
2. Iterative identification and clustering methods were used to determine 12 chromosome-specific centromeric repeat sequences (CSCRs). FISH technology was used to identify centromeric characteristics, further revealing that transposon insertion events play an important role in centromere structure formation in avocado.
3. Genes related to disease resistance (NLR genes) and fatty acid biosynthesis were identified, with specific expression of Pa07g1095, Pa07g1091, and Pa12g0002 (FAD2 gene) observed during the triacylglycerol (TAG) formation phase in fruit. This study provides new insights into fatty acid biosynthesis in avocado.
Example of T2T Genome Assembly Results
Frequently Asked Questions about T2T Genome Assembly
Q: How does T2T genome assembly differ from earlier genome sequencing efforts?
A: Unlike traditional assemblies, T2T genome assembly captures every base of the genome, including regions that are usually hard to resolve such as telomeres and centromeres. The result is a gap-free sequence that offers a more complete and accurate view of the genome.
Q: Which sequencing platforms are used for T2T genome assembly?
A: The process mainly relies on PacBio HiFi and Oxford Nanopore ultra-long read sequencing, both of which generate reads long enough to span complex genomic regions. Short-read sequencing is often added to increase coverage and refine accuracy during the polishing stage.
Q: What does "polishing" mean, and why is it necessary?
A: Polishing is the step where additional data, either short or long reads, are applied to the draft assembly to correct errors and sharpen accuracy. This ensures the final sequence is as reliable and precise as possible.
Q: What are the biggest hurdles in T2T genome assembly?
A: The toughest areas to resolve include telomeres, repetitive elements, and regions with high variability. These require optimized algorithms and advanced data handling to piece together correctly.
Q: Why is T2T genome assembly valuable for research?
A: By producing a more complete genome, T2T assembly deepens our understanding of genome architecture, gene activity, and genetic variation. This level of detail supports discoveries in genetics, disease mechanisms, and evolutionary biology.
Q: How does T2T assembly impact telomere and centromere studies?
A: Telomeres protect chromosome ends, while centromeres control chromosome separation during cell division. Having accurate sequences of these regions makes it possible to study chromosome stability, aging processes, and mutation-driven disorders in greater detail.
Q: What is the ultimate aim of T2T genome assembly?
A: The goal is to deliver a fully assembled genome with as few gaps as possible, ideally zero, covering all parts of each chromosome including telomeric and centromeric regions.
Q: Why can't zero gaps always be achieved?
A: Some chromosomes contain regions that are extremely challenging to assemble, meaning small gaps may remain. While T2T strives for a seamless sequence, the realistic target is to keep gaps to an absolute minimum.
Q: What role does Hi-C sequencing play in the process?
A: Hi-C data helps connect contigs into chromosome-level assemblies, resolving large-scale structure and ensuring accuracy. It also serves as a way to check the overall quality and completeness of the genome.
Q: What types of samples work best for T2T assembly?
A: High-integrity DNA is essential. For plants, young leaves or tissue culture material are ideal. For animals, whole blood or fresh internal tissues are recommended. DNA should be long, intact, and free of degradation or contaminants to guarantee high-quality results.
Related Services
Send a MessageFor any general inquiries, please fill out the form below.
